Hey Jazzy, I had the same issue awhile back. On my Series instruments, I run the bridge through a Crown amp, and the neck through a QSC RMX (the really heavy one). The Crown is very clear, but with the digital switching, it somehow does not bring in the low end warmth that the QSC brought to the mix. As far as the preamps are concerned, I use to have them all the way up, and turned the volume down to. I then read somewhere, that the gain mid position is the starting point. Full up was best for headphone output, mid was best active output, and low was to match a passive output. So, I backed them off to about 60%, and the distortion went away. Maybe using the volume control just makes the distorted signal quieter, if that makes any sense. Hopefully some of the pros here can give you a better answer, but this worked for me. Cheers!
Joe