I have been fighting with M60s and Denon 3805 sounding too harsh for a while. With rock and metal music the combo often sounded harsh (think Slayer solos).
I have found that adjusting the pre-amp channel levels to set the mains at +0dB (was previously +6dB) has helped tremendously, even when playing at the same calibrated volume level(using a dB meter) in Direct mode. The preamp may have been inducting some minor distortion I guess?
Also if you are using Audissey or any other EQ you should ensure that you do not have any significant bumps in your curve. I would re-run your test will all EQs disabled.