Yes, I cleared everything from the stomp section, running as direct as I can, even tried from the alternate input without success. Going to a friend's house with my guitar and the profiles I'm using here on a USB key to compare with mine. Will keep you posted. Thanks!
Parallel path on/off is actually in the Rig menu even though it affects stomps A and B. Even if those stomps are bypassed it is still possible for parallel path to be causing two separate signals.
the massive volume difference on the second rig is because it is a clean rig and the others are distorted. This means that you clean sens control is set too high. Turn it down to about -7 (Then fine tune to taste) and it should sort the issue for all clean profiles.