I have a Pitchfactor and it doesn't slaughter my tone at all. I run it through a Bogner Ubscherschall with a pretty hot signal coming out.
Did you check your input meters? Also, do you have the correct Input/Output switches set correctly? You will want it to match your effects loop.
Also, do a quick a Google search on JCM 2000 effects loop. It appears many people have issues with these loops.