the usual solution to this is to check the signal path.
if you haven't done this already, try:
1 record your source through one of the mixer channels and feed the main mix output of the mixer into the soundcard
2 take the output of the soundcard and feed it into the tape/CD input of the mixer
3 switch the control room output to this input only
4 send the control room output to your monitors or headphones.
Doing this means that when monitoring you are always listening to what comes out of the PC, and you will be able to record a second track without the first recording along with it