It seems that no matter what pedal or type (even a delay) plugged into the bias head effects loop completely changes the original patch tone. Am I missing something? Sounds like mud until I unplug the loop.
I don't own the head but a common cause for this is in many amp FX loops is incorrect levels. Some effects loops operate at line level and many effects operate at instrument level. Make sure you have things set correctly as a first step before any further debugging.