Could CCleaner and a malware scan cause serious problems in Windows?

Anonymous March 20, 2014
Ads by Google

So I ran a system and a registry scan on CCleaner and a full malware scan on Malwarebytes. After both were done, I saw a dialogue box asking me to reboot my computer to save all changes.

When the computer loaded back up, the Aero theme has been disabled without a way to re-enable it, the audio doesn’t work, the background is no longer what I set it to be, and I cannot connect to the Internet at all.

I’m wondering what possibly could cause this problem, and what I can do to fix it?

Any and all help is much appreciated.

  1. Abilash A
    March 24, 2014 at 5:21 pm

    Obviously NO, they don't cause a problem. I have been using them side by side

  2. Oron J
    March 22, 2014 at 10:10 am

    I'm "joining the party" rather late here. There are many good points raised, and I think Jan raises some particularly good ones. So, looking at things in the round:

    • CCleaner cannot affect Ubuntu.
    • Malwarebytes Anti-Malware found some items, which suggests that you had malware on your computer.
    • Your computer is running much faster, so whatever happened, some problems were resolved.

    I'd like to put in a good word here for CCleaner and Malwarebytes. They are both excellent products, and although there is no need to clean the registry regularly, CCleaner is very safe. I've never seen it cause any major damage, and of course it makes a backup file.
    I don't think they are likely to have caused the problem directly. More likely, in the process of resolving other problems, they have exposed some underlying problem. I like Jan's hypothesis of bad hard disc sectors, it makes a lot of sense, but it could also have been caused by the malware, which can't always be removed successfully. Think of it as a medical operation. Sometimes the patient is just too sick, and the operation may be successful, but the patient...

    So, what can you do now? As suggested, running SFC and reinstalling device drivers would be the next logical step. If that doesn't work, reinstating the old registry entries (i.e. double clicking on the CCleaner backup file). Also, you may want to check your hard drive for any problems.

  3. Hovsep A
    March 21, 2014 at 7:29 am

    well if your pc is infected and registry keys infected then anything is possible CCleaner perhaps is not suitably armed to deal with this situation, also the same for Malwarebytes concerning false positive. Normally you should go through scan details to check for false positive for example. Some spyware cleaning can cause the problem.

    if important drivers, files were deleted and restore point cant help then you have to replace the files perhaps by reinstalling windows.

    superantispyware had some Repair options in System Tools Section?

    1) reset your router
    2) open cmd with administrative rights
    3) type: ipconfig.exe /release and hit enter
    4) type: ipconfig.exe /renew
    5) type: netsh winsock reset catalog
    6) type: sfc /scannow

  4. Jan F
    March 21, 2014 at 6:12 am

    If both operating systems where affected, Windows and Ubuntu it couldn't possible be CCleaner as it solely cleans the registry (which Ubuntu doesn't have) and it only cleans temporary files and clutter within Windows specific directories.

    That leaves us with Malwarebytes which, as the name suggests, is there for cleaning malware. So if it did find something to remove you had some form of virus or trojan on your system.
    Therefor, the least thing you should do is using System Restore. In fact you should remove all system restore points to make sure the malware doesn't hide in there and run another scan across your entire system.
    One thing that comes to mind is changing all your passwords using a different computer.

    If you don't recall malware bytes finding and cleaning something another option would be a hardware fault.
    Now, by default Windows should not be able to access the file system used by Ubuntu ~ unless you were using FAT32. However, Ubuntu is capable to access Windows FAT* or NTFS file systems.
    You removed something from the hard drive, now things run better under both. That leaves the chance of some files or folders residing on bad sectors which can indeed cause performance problems as the OS may try to access the data and get stuck in a read-failed-retry loop for some time.

    My suggestion would therefor be to run a full check disk scan within Windows, check the SMART values for reallocation events.

  5. Jeff F
    March 21, 2014 at 5:00 am

    It's possible that removing the malware caused system instability, that's actually quite common. However, there is very rarely a legitimate reason to "cleanup your registry". Please refrain from using this feature in the future.

    • Cristián T
      March 21, 2014 at 5:38 pm

      Thanks for letting me know! I'll keep that in mind next time I run scans in CCleaner.

    • dragonmouth
      March 21, 2014 at 8:53 pm

      "However, there is very rarely a legitimate reason to “cleanup your registry”. "
      No reason other than thousands of orphaned Registery Keys which could cause instabilities and problems. Windows has never been good about deleting keys left over after an uninstall.

    • Jeff F
      March 22, 2014 at 3:45 am


      The only issue I've ever had with orphaned registry keys is that they sometimes cause the Program Manager to list programs as still being installed when they were actually removed. Other than that, they just take up space. They don't break your computer and it's totally normal. Registry cleaners, in my experience, DO cause more harm than good.

    • Bruce E
      March 25, 2014 at 12:32 am

      Orphaned registry entries can cause various systemic problems and performance issues. Cleaning the registry can result in a measurable performance improvement in several areas. After some uninstalls, the orphaned keys can result in Windows looking for software that no longer exists on the system (wasted I/O) which can have a big impact on startup and login times (HKLM, HKCU), they consume more memory when the system is running, file associations can become messed up (HKCR) causing the system to fail to open a program at all or to open the wrong program for the file, etc. Just by fixing these types of problems, I have been able to cut boot times on some systems by almost half.

      That said, one should not play around in the registry if they don't know what they are doing. This applies to using registry cleaners too. Many times, an entry may appear to be orphaned because the program that uses it - sometimes Windows itself - uses the entry in an unconventional manner. The only keys one should mess around with are those where you know EXACTLY what they key is for and how it is being used. As long as one plays by these rules, you should not run into any kind of irreversible trouble if you manage to find trouble at all.

  6. Dalsan M
    March 21, 2014 at 12:53 am

    Try to restore your system to a previous date, and/or restore the registry from the (hopefully) saved CCleaner registry backup, just double-click on the registry backup that was created after locating the file in the saved folder.

    Registry cleaning is not recommended very much anymore, especially due to the reasons you are mentioning and worse. Registry cleaners hardly do any good, especially for performance, and instead creates a higher chance of errors occurring. Unless you have a pretty good knowledge and understanding of the registry items, it is best not to mess with it or else you may have to deal with the effects, including not being able to boot into Windows at all.

    Malware scanning and cleaning usually does not cause errors, but that does not mean it doesn't happen, especially if you have modified any system files or installed programs that may alter system files.

    • Cristián T
      March 21, 2014 at 2:05 am

      The reason I ran those scans was because my computer was running extremely slowly with a lot of lag, which also seemed to have affected my other operating systems. After the reboot, my computer was running on noticeably higher speeds, both on Windows and my other operating system, Ubuntu. Obviously the problem at hand is the fact that on Windows, there is, as of now, no way to access the Internet, listen to audio, or change the Aero theme settings.

      I am highly hesitant on using system restore because I'm afraid of my computer becoming slow again. Would that be something I should worry about?

    • Dalsan M
      March 21, 2014 at 6:58 am

      Now that we know there was an affect to other installed operating systems both prior to and after cleaning and scanning, I would follow Jan's suggestion. Do you remember if there was any malware or threats that were found by Malwarebytes? I'd suggest using an antivirus to scan your system, as well just to make sure that your system is free from malware. You could also try out Windows Repair (All-in-One) to see if it can help, and use sfc /scannow from the command line.

    • Bruce E
      March 21, 2014 at 7:34 am

      Affected both operating systems? Is your second OS running in a VM or are you dual-booting? If you are dual-booting, the changes make by CCleaner and Malwarebytes should not have affected the performance of Ubuntu since Windows cannot access and make changes to the ex4 partitions a default install of Ubuntu would use.

      Open an administrative command prompt and run the command 'sfc /scannow' This should replace or repair any files that may have been deleted or damaged during malware removal. Reboot if anything was replaced.

      If you still don't have Aero effects, audio and network after this, open up Device Manager and remove your audio device, network adapter and video driver. Reboot the system and allow it to reinstall those three drivers.

    • Cristián T
      March 21, 2014 at 5:37 pm

      @Dalsan I remember there being several threats detected by Malwarebytes. Also, are there any good free antivirus programs that you recommend I download? Once I get that, I'll perform an antivirus scan, try Windows Repair (All-in-One), and use sfc /scannow from the command prompt, and let you know what comes up.

      @Bruce I am currently dual-booting Windows and Ubuntu. As I said to Dalsan, I will try sfc /scannow in the command prompt (with administrator priviliges) and reboot. If that doesn't work, then I will remove my audio device, network adapter, and video driver from the Device Manager and, again, reboot, and I'll let you know what happens.

    • Dalsan M
      March 22, 2014 at 7:56 am

      Avast, Avira, MacAfee Stinger, Clamwin are all good antivirus software to use (Stinger should be used after other antivirus scans to make sure that your computer is free of rootkits and other deep infections). Panda Cloud free and Bitdefender free should work decently, as well. If you choose to scan with Clamwin, expect to wait many hours before it finishes as it will scan just about every file thoroughly.

      If you have Hiren's Boot CD or Ultimate Boot CD, use those as they usually contain several antivirus software, and may be able to access files more easily than if you were to boot into Windows. I would also backup any important files as a precaution, just make sure they are clean and safe before backing them up.

    • Cristián T
      March 24, 2014 at 7:05 pm

      @Dalsan Since I don't have access to a blank writable DVD, I have resorted to a 32 GB USB flash drive for booting into HBCD, but I get BSOD after attempting to boot into MiniXP. The BSOD occurs while the OS is loading files. The computer in question is a Dell Studio 1558 laptop.

    • Dalsan M
      March 25, 2014 at 12:13 am

      You can try Avira Rescue CD or other rescue CD from a reputable antivirus software company, of course creating a bootable USB out of it. Without Ryde BSOD error codes, it is more difficult to tell what you can do to prevent it.

  7. dragonmouth
    March 20, 2014 at 11:46 pm

    Both CCleaner and Malwarebytes have several options, "Remove" or "Delete" being among them. If you ran the programs with some sort of a Remove option, Registry Keys and config files could have been deleted, causing your problem.

    • Cristián T
      March 21, 2014 at 1:56 am

      Alright. It's good that we are now aware of what is causing the problem. The next part is, how exactly do I fix the problem so that Windows can function normally?

Ads by Google