Try adding more rugs, covers, etc. to your room to soften its acoustics. I've found that scattering cushions around the room works quite well. Try not to have any hard walls exposed in the room, as these will increase harshness.
I don't know anything about your speakers/equipment. Perhaps:
- Your speakers might not be putting out enough bass at high SPL (105-115dB) levels.
Solution:
Route more bass/sub-bass to the subwoofer, if the subwoofer is sufficently powerful.
- Your speakers are distorting heavily at these peak levels.
This might not be the problem, as short periods of distortion are inaudible. Did the speaker sound good when you bought them?
- Your amplifier is clipping at these peaks.
Same as above except for amp.
I have also read that amplifiers can distort during transient peaks, but I'm sure mtrycrafts would disagree with that!
One way of removing system brightness is to use the tone controls. I've found a boost of 6dB at 100Hz and a cut of 6dB at 10kHz sounds quite pleasing at -6dB (to allow a little headroom for the bass boost). You could try using the THX re-equalisation on your amplifier if you've got it, as this is meant to 'remove the edgy brightness' of film soundtracks. Denon's cinema equaliser does something similar, though I don't think it sounds that good.
A good reference quality DVD to try your system out with is the Star Wars trilogy and Star Wars episode II.