If you use a tube power amp you need to turn off the power amp modeling. Otherwise it will be boomy and harsh since you are going through essentially two power amps.
I did in fact try turning off the amp sim but then it sounded completely dead. I was not really pushing the power amp at all so was hoping it was falling short of really coloring the sound. The GT1000FX should remove this variable completely so hopefully it is that simple. It probably is.