Matt, the fact that you specifically mentioned explosions and similar dynamic sounds as causing a problem would lead me to propose that the poor sub is the most likely suspect, far more likely than the 805, which has a quite powerful amplifier. As has been suggested, you might at least temporarily set the sub to "No" so that the M60s would run full-range and would be handling the LFE plus redirected low bass from center and surrounds. Putting all of this burden on the M60s wouldn't be ideal, but you might at least try and see if the absence of the sub would lead to a net improvement.
As to your concern whether the Audyssey equalization is being affected by the poor HTIB speakers and resulting in a poorer adjustment for the M60s to try to compensate, you might try setting Audyssey so that it doesn't affect the front speakers, but equalizes the surrounds to more closely match them. With adequate setup and experimentation the majority of users indicate satisfaction with the improvements that have resulted with Audyssey.
