Also are you useing speakers or headphones as you could be getting some feedback if using speakers whilst flying which you wouldn't in the quiet of the tower.
You may have done this already but:
.radio 5 mister fork
will tune radio to you so that you can talk to yourself.
I had similar problem, upgraded my soundcard drivers and the surround mixer (I have a soundblaster Live card),
I now have the Pretty blue surround mixer (surmix2) not the black and yellow one (surmix)
Only problem I get now is very occationally my Mic boost doubles instead! so I'm never quiet
