I can pre record a wav file using windows sound recorder and load
that in to Guitar FX, and it seems to work fine. But even while that
is playing and i start playing as well the fx only take place on the
pre recorded guitar. The other guitar just comes through clean as
though its not going through the Guitar FX program at all.

Im using Windows XP, and the sound card is an, Advance AC97 Audio
that is built on to the motherboard.

Any help would be apprectiated!