Roobin: I tried your advice (low master volume, low wet mix on the boogie (a few %) and a low mix on the Timefactor/mod with killdry engage) and it worked marginally better. I could get away with playing a few notes beore the rumbling sound started coming out. Unfortunately, even though this setting is slightly better, the effect is far too low for even bedroom playing and in the Killdry mode when the effect is bypassed I get no sound out of the amp.
DGillespie: Between my effects I use Evidence patch cables and between the loop Send/Return and my pedals I use Planet Wave cables with the gold tips. Some pedals seem to work fine in the loop while others have issues.
I spoke with a Mesa/Boogie rep and he suggested I switch the loop from parallel to series. I hope this fixes the problem. Do you guys have any other suggestions? Thanks for all your help thus far and if I do get the loop changed I'll definitely let everyone know. Thanks again