its because the 1/4 outputs bypass the output tranformers-- at least thats what i've heard on the net--they say use the 1/4 in .they sound better--is that what you think

what tubes are you using

I know Peavey uses Pin 3 Hot on most of their Live Sound Gear, and the VMP2 is likely included. I don't see why swapping the relative phase of a single channel would have that drastic of an effect, but it is something to look into :)

Mike, are you saying use the 1/4 " inputs ? They are unbalanced. Did you mean 1/4" outs ?
BTW, I'm using stock tubes. I have some mullards in my Drawmer 1960 I like. I may swap just to hear the difference, but the VMP2 is REALLY quiet with tons of headroom as is.

yea its the outputs that have a different sound-use the 1/4inch outputs better