Audyssey and Tritons

Anyone have experience using Audyssey Multi EQ with a system running Goldenear Triton 1s?  They don't seem to play well together. It wants the subs turned WAY down before it will even run. Then, it somehow thinks they are small speakers. And while it gets the distance about right for the L and R mains, it thinks the subs are way farther away. 
So...any thoughts? In fairness, it comes out sounding  pretty ok. Except the subs will be way too low for music running straight.