I've had this issue before, but it was always the laptop going back to it's 1 channel default mode for the input. This time, however, the computer is not to blame, it is the software. I double-checked to make sure the input on the computer was set for 2 channel/41000, and I also recorded on to Cool Edit Pro to make sure the stereo setup was working, which it was. Any ideas? Using Windows 10, by the way.