I know I'm resuscitating a 5-year old thread but since it helped me I thought I would reply here.
I basically had the same problem as the original poster: been using a Denon AVR-X4000 for a while, and I always found the sound quite harsh. The highs were literally hurting close to reference level, and given my rather small room has dual PC12-Plus, bass was quite a let down. For years I thought this was a "balanced" sound, and blamed the untreated room for the harshness. I do indeed have a second home theater in the basement, with much cheaper speakers, powered by an Onkyo TX-NR818, and the sound is so much better there -- fuller, not painful, etc. -- it's not even funny. But it's also a small, fully carpeted room with textured ceiling, so that helps.
Anyway, having heard other home theater setups recently, I decided to see if I was doing something wrong with the Denon. I've re-ran Audyssey multiple times over the years, but I decided to try the microprocessor reset trick that time.
Well, just a word of warning: this is a full factory reset of the receiver. You'll have to set all the inputs up again after this. And you have to re-run Audyssey afterwards as everything is deleted. Now I decided to run Audyssey a little differently this time, with the 8 positions more grouped around the main listening position, and with the 4 last positions on the forward edge of the seat (I've never included positions that forward before).
So I can't tell if it's the factory reset that helped, or the new Audyssey positions, but it did make a major difference. I now have plenty of bass and mid-bass, the thing that I was after during years. And the highs are no more harsh. So I'm pretty happy with the setup now -- but it took me so long to get this right that I fear many people would have either changed their AVR or just stopped bothering.
Another thing: I've discovered that audio parameters, in particular the subwoofer trim level, is applied and remembered on a "by-audio mode" basis, not by-source nor a mix of the two. There are some exceptions: for example, Dolby modes all share the same parameters. But this could be confusing if you adjusted your sub trim level for movies and now found out that music is not that fun. It may be that the sub trim is back to default.
This is handy to fix the Multich Stereo bug. It seems to me that in this mode, the Denon X4000 is sorely lacking bass. I suspect that the only bass redirected to the sub is from the L/R channels, since it's a stereo signal, and not all channels currently playing. Thus, assuming 5 channel, that mode would lack 20*log10(5/2) = 8 dB. That peculiar correction can be applied for the Multich Stereo mode without affecting the other modes.
Anyway, many thanks to you, 2014 posters.