I had an audio issue a little different than yours, but what it ended up being was a resource conflict in windows between my usb audio input device and *something else,* I switched to using the port on the motherboard and that fixed it. So I would recommend unplugging everything except what is strictly required, to make sure it's not a device conflict.
My problem was real weird. When the conflict happened, the audio would cut out of the recording, but not replaced with black, just more audio from where it came back. So a 2 hour audio recording would be 1 hour 59 minutes long file with weird glitches. I had to use an external recording device to check. That device created a 2 hour file for 2 hours of recording, as you would expect.
