Lot's of good info here on the GNX...
Guitar Workstation® :: Index
I did have problems using an E-MU USB midi on my GNX3. It caused a lot of USB injected noise while the Genedit app was running. It worked fine on my GNX2. However the noise could have been picked up by my Fender Pro Jr, and may have had nothing to do with the GNX3. I never bothered to check it out because I had a sound card based midi hookup as well.
I can't stress how much easier it is to use the genedit software vs. manual tweaking of the controls. It's very complicated to get a great tone. One reason is that the cabinet models seem to need a lot of adjustment or the sound seems dull and muted. The software makes it a breeze.