Put just a short cable in your effects loop - that should be a pretty easy test to diagnose if it's something in your chain pedal-wise, or something in the amp.
Regarding Les' comment on the line level signals, I've also had that problem. More manufacturers are starting to add a switch to their amps that takes the signal down to an instrument level, including the discontinued PRS SE amps. Personally, I would rather have the switch than the adjustable dials that USA PRS amps have, it's just so easy. I'm sure there are reasons to have the fine adjustment too, I just don't need them. And it's all about me!
Any amp maker that's still making a fixed, line level loop is committing a crime, IMO. Seems like the vast majority of players are using pedals, not rackmount stuff. But maybe I'm missing the big picture. After having my PRS amp, I will be HIGHLY resistant to ever buying an amp that doesn't have an instrument level loop, and bias test points. C'mon, do we all REALLY need to be paying $50-100 to get our amp biased every time we change tubes, when we could just get a multimeter at Radio Shack for $20?
Sorry for the rant.