Have you tried pulling down either the "Vol" or "Mast" parameters? I guess I would assume with settings that high, you might even start running out of the amp model headroom with high output pickups and hear some squish and/or distortion with heavy playing. Kick on an external pedal and it would get worse. I'd try dropping those numbers slightly and increase the "Output" parameter to compensate for volume if you need to.
Or, try your pedals into one of the other clean amp models and see if you notice the same thing.... maybe one of the digidesign models like modern clean.
I can make the MS-30 model, the bogner clean model, and the soldano clean models all breakup (no external pedals) with settings in that range.
What were you using before the 11R?