BLOOZMAN,
Hey I took it one step further, I just dimed everything out. I then fiddled with the loop. I had it in, and then out. I adjusted the loop volume, and I came to this conclusion. I notice that with the loop in I get some feedback, not much, but a little. I just backed up, and problem solved. I also noticed that there is no issue with the amp in "hard bypass" mode. I also took my delay (line6 DL4) out of the loop, but left the loop active. BINGO... lots of feedback. When I placed the delay back in, a closed loop in essence, there was not much feedback, a little but not annoying.
One thing to consider is that I have JJ tubes through out. I use a 12AT7 for the reverb driver, and have 5751s in the V1 and V2 spots. The JJ EL84 power tubes may have everything to do with the feedback. The JJ's are designed for high gain applications. I do not have a rippin amp like JJ/Tesla had in mind when they designed the tube. this may be an advantage over the Russian MESA tubes.
On a side note... You should try putting 5751 tubes in the V1 and V2 spots. This really makes the cleans have a little more headroom. I also run a 12AT7 for the reverb driver. I noticed a significant improvement in tone when I replaced the MESA tubes with JJs.