About a week ago I figured I would give Audyssey XT another try in my room since I've added 2 small monster traps, ceiling treatments and rear wall treatment. It took a little work but the results have been very good or even better than without Audyssey. I've always followed the Audyssey Guide steps and never could quite get it to sound right. The last time I ran Audyssey was before some of the traps/treatments I mentioned above and the response from 20hz to 40hz was down 5-6db - other times it made my previous main speakers sound lifeless with no bass. I had some similar issues this time too but was able to resolve - more on that later. I ran Audyssey following the Guide as I always have: staying outside the room during measurements/chirps, mic placements, ensuring fans/Hvacs are off, etc etc.
When finished Audyssey crossed all the JTRS up front at 70hz and my rear dipoles to 60hz. I moved them up to 80hz, the LFE channel was set at 80hz by Audyssey and I left it there. The distance measurements were spot on. Audyssey set the trim levels of the JTRs at -12, the rear dipoles were at -3 and + 1 and the Sub at -10. I should note that the SubMersive was previously EQ'd by Anti-Mode and the level was set at 75db at reference prior to running Audyssey.
I then engaged THX Cinema mode which is what Chris from Audyssey recommends using with the Onkyo 805 and Audyssey XT for movie listening. I popped in X-Men First Class to see if I can hear a difference. The difference was subtle in some areas better in others but all was an improvement - almost all. Dialog seemed to be even clearer, sound panning across the room seemed slightly more fluid. Highs seemed to sizzle more but in good way as it was more pronounced yet not ear fatiguing. Midrange seemed improved - a tad smoother or more natural to my ears. Now for the Bass.The bass was GONE!! And I don't mean Gone in the sense that You aint used to reference bass gone but more like "who the hell turned off the SubMersive?!" gone. I then pulled out my SPL meter to check the levels using the receiver internal test tones. The SPL meter was set to C-weighted and slow. All channels matched up perfectly. WTF?! This cant be right! I can see not having enough bass but this was literally like having the sub off or barely operational. I mean my local Non IMAX Movie Theater has way better bass levels than this and that system sounds weak. My local IMAX, on the other hand, sounds great for in the bass department.
I decided to pull out my Real Traps test disc to check out the frequency response. The Real Trap test disc does Hz in 1hz increments from 10hz to about 250hz. The Real Trap test disc revealed that my uncorrected response from 18hz to 78hz was +/-3db. By the time I hit 78Hz, the db started to rise. From 80hz to 110hz the response was 7db more than the response below 78hz. I started spot checking 120hz, 130hz, and above and there were all about 6-8db higher than the response below 78hz. I then decided to pop in the 5.1 Audio ToolKit that came with my SubMersive. Those of you who have this disc know that as it starts up, there's music that plays and it has a bass line to it that's sounds clean. As soon as I put this DVD in, I noticed everything sounded a tad cleaner/clearer and a little more spacious but the bass was not there either. I went through the first couple of tracks on the disc in Dolby Digital mode and the all the main channels matched up perfectly but this ToolKit indicated that the
.1 channel or LFE was 7-8db down then the rest of the channels.

I went back into the receiver to double check the internal tones and the receiver once again stated I was matched all the way across on all channels. Went back again to the 5.1 Audio Tool kit and it indicated down 7-8dbs for the Sub.

I decided to raise the SubMersive volume dial up 3 clicks and raise the Sub trim level in the AVR to from -10 to -7. I can finally hear the bass but it still a bit quieter than what I like. I then raise the SubMersive dial up another click, set the sub trim to -6 everything is now flat according to the SPL Meter and Audio ToolKit. The music on the Toolkit sounds great very balanced, but maybe just a tad less bass then what I prefer so I raise the Sub AVR Trim from -6 to -4.5. Now it shows the Sub as being ~2dbs hotter than the other channels and sounds much better to my ears. Next I engaged THX Cinema mode and noticed that it adds another db to the bass while removing a db or two from the surrounds. This was all verified via SPL meter and Toolkit dvd.
We then watched a movie and I noticed an overall improvement. The bass seems a tad bit tighter sounding with Audyssey XT and Anti-mode then with just Anti-mode. I triple checked everything again and the Audio ToolKit shows 2db hot on the bass, Real Traps test disc shows it fairly flat response maybe a db or 2 hot for bass and the Receiver internal test tone indicate I am now 9-10dbs hot

Who's to say which one is right or wrong. Some searches I've done on the Audyssey thread indicate the receiver test tones along with what Audyssey did is accurate. I then searched the SubMersive thread and found a post where Mark Seaton states
"I often find the values I get with the DVD differ from what I get with internal test tones, and I always trust the DVD over the pre-pro/receiver." What's important is my ear prefers it this way and I would be willing to bet most that like a flat response would only want to back down the bass by 2 maybe 3db from where I currently have it.
We have since watched over 10 movies after the change and I can now say I am finally enjoying Audyssey XT. I can even watch a movie at quieter levels now and the dialog is still very clear not that it wasn't before but its even better now.
PS. I actually made notes the last time I ran Audyssey and it looks like there was the same discrepancy with the Receiver test tones vs the Audio Toolkit then too. I probably just never bothered paying that close of attention to it because the response back then was down 5-6db from 20hz to 40hz so I just gave up on it. Maybe all of this is a bug in my receiver than can be fixed with a firmware but I'm happy enough with my manual adjustments to just leave things as they are.