When I record with ANY screen recorder (by which I mean all the ones I have tried; the list is quite extensive), after a few minutes the audio will go out for a few seconds and a HUGE blip of distortion will occur. As in, ear-deafening with headphones on. Everything will then continue as normal, though odd blips will continue to occur, though not nearly as loud.
I at first thought it was the screen recorder (I believe the first time it happened I was using Camstudio), but as I continued to try them, it continued to happen, and I was forced to conclude it was my computer.
I presently have Fraps (paid), and the same thing continues to happen. Some things I’ve thought of are the computer freaking out because it doesn’t have enough resources (though this seems rather unlikely), and the microphone sucking (though this doesn’t happen during voice calls).