I have a Boss GT-8, using the 4-cable method, with a Peavey Valveking amp head. I've noticed whenever I hook it up, it changes my tone. I've disabled the preamps, all the effects, neutralized the global EQ, played with the output, everything I can think of, and my tone is still a lot sharper than it is normally. It's like I get a giant presence boost or something.

Could this be bad cables? A problem with the levels? Loop placement in the effects chain? I can't figure it out. Anyone had a similar problem and solved it?