I think what you're hearing is phase cancellation caused by mixing the original signal with an A/D converted signal .The A/D signal is very slightly delayed and out of phase with the original. This is the problem with parallel loops. In my experience all you can do is have your loop modified to serial…  or get another amp…sorry not good news but I've been through all this. Most amp manufacturers realize this nowadays. In the old days the theory was that a parallel loop ensured that your original incredible tone to die for was intact…they now know that with digital effects in the loop parallel sucks.