There are a few things going on here.

First, your crossover settings are WAY off, and that could certainly be causing some standing wave issues. I know your mains are full range speakers, but try the crossovers across the board closer to 80hz. I think you'll find it smooths out the sound quite a bit. Your surrounds, for example, are rated to 60Hz. Your crossover freq. should be a min. of 10hz above that point--and possibly higher. Even the fronts are rated to around 35hz, which means your crossover needs to be the 60hz setting. However, even at 60hz you're likely to get some odd issues between the bass produced by the front mains and the sub. You'll have to experiment a bit, but 80hz is likely your best bet for all speakers.

Second, I've had similar problems with my Definitive Technology sub, specifically with the first LOTR movie. What was happening is that I was experiencing a huge null at around 40hz, so I was pumping up my sub to compensate. However, that created a huge peak (15 or more db) at 50 or 60 hz. So when movies were loud (they can reach 100db when calibrated properly), certain frequencies were way above that point--clearly greater than almost any sub can handle.

The solution was twofold--evening out the crossover frequencies, and moving the sub. The combination of the two eventually eliminated most of my standing waves (I still have some nulls, but they're not nearly as bad), and I made sure I calibrated for the loudest frequencies, not the quietest. Then, I tested with a number of movies, and made the final adjustment by ear, making sure that movies with the loudest bass (LOTR, Star Wars AOTC first scene) didn't overload the sub. So now, for example, the tank-tapping scene in Finding Nemo is impactful, but not as earthshaking as it could be, but the spaceship in AOTC doesn't distort, either. You have to find a balance in an imperfect system.

I used to get the bottoming out from the THX logo, as well, and in some of the heavy bass scenes in Eternal Sunshine of the Spotless Mind. Now, properly placed and calibrated, the sub sounds great, and I never bottom out. I hope this helps.