Roobin: I tried your remedy (low master volume, low wet mix on the boogie (a few %) and a low mix on the Timefactor/mod with killdry engaged) and it worked somewhat. I could get away withplaying an few notes and no odd sounds but if I were to play quick notes in succession the problem returned. Not to mention, on Killdry mode when an effect is not engaged I can hear nothing through the amp at all. I guess in this mode it needs an effect for it to work?
DGillespie: Between the pedals I am using evidence patch cables and between the pedals and the loop send/receive I am using planet-waves with the gold tips. Some pedals work fine in the loop while others have problems. It seems like its hit or miss.
I spoke with a Mesa/Boogie rep and he suggested I change the loop from parallel to series. Do you guys have any other suggestions? Thanks for all your advice so far. If I do get the FX loop changed I'll definitely keep everyone posted.