Ok, so I'm having one of those "did you try to plug it in" moments. I went into workbench to check and see if maybe I had the magnetic pups blended with the modeled pups and low and behold, it was set at 10% blend.
I took it down to zero and problem solved. Feel like an idiot because the manual and this forum has many posts about not being able to use altered tuning if you're blending the pups.
Although I don't recall reseting the blend but whatever. hope no one else is having this problem!
Miroslav - Thanks but I have the latest firmware installed (I think it's 2.6).
I've mostly corrected the problem with some trouble shooting and borrowing advice from other issues posted in the forum. I have the 4CM setup per normal configuration. I have Input 1 set to Variax and Input 2 set to Variax Mags. I then split the signal, put the FX loop in path 2, and played around with the input/output settings of the FX loop. That's addressed the overall issue of nasty feedback. I still get a little noise when engaging Marshall dirty channel but I figure with some more EQ fun I'll get that fixed.