Craig,

I suggest reading the information on Audyssey's website because it sounds to me like you aren't using the correct settings based on their recommendations.
I was also using many of the wrong settings before I understood what was really happening with my personal setup. I am no pro, just a dumb sparky with a laptop and the internet.

After running Audyssey you would think that everything would be setup correctly; however this isn't the case.
A prime example is the large vs. small argument.
If a sub is in your setup, your receiver will set your speakers to large if they can handle low frequencies. This is the wrong setting according to Audyssey. The receiver manufacturers are stuck in a time warp and are dumb as a brick when it comes to this!

As Freddy mentioned if you have a sub in your system your speakers are small. There is no argument to this according to Audyssey.

[Link: audyssey.com]

In regards to your setting LFE+Main.
This is a quote from Chris Kyriakakis from Audyssey, "LFE only.  LFE+Main is a bad setting because it overlaps the bass in the sub and speakers resulting in boomy bass."

[Link: audyssey.zendesk.com]

Again, I highly recommend reading the information at Audyssey. You will find as I did that your receiver isn't exactly helping when it comes to bass management.

After understanding and implementing the settings suggested by Audyssey I can say that My Denon 4520CI has never sounded better.
Now if only we could get the manufacturers that use Audyssey to set things up correctly!!!!