Hi
Yer I had the same kind of proplem.
i often wondered why peop;le mike there amps through computers? and thats the reason because unless you have a dedicated computer for sound only there is allsorts of weard and wonderfuly things going on in the background.
Say that I managed to improve mine a bit by running my guitar through a Di box with The XLR output on the box.
This was a slight improvement if I want to record I mike my amp up and record that way, it is also much close to the true sound you are playing.
hope this helps.
Barry