I think you're talking about the AMC Mercado, and I agree that the sound that you get in those theaters is pretty lousy. Dialog intelligibility is terrible considering that the theater is only about six years old, and the surround speakers are mounted in some weird overhead position so the surround effect also sounds strange. (Why that theater is among the top grossing theater complexes in the U.S. is beyond me) Someone I know who works as a sound engineer speculated that some AMC theaters sound the way they do because a lot of them use composite screens that are less acoustically transparent than what you typically find in other theaters. (He also mentioned that the new HPS-4000 installation over in Waikiki is the best movie theater sound system that he's ever heard) Those composite screens are supposedly better for image quality and brightness, so you might have a trade off.
For my general moviegoing, I just go to the Century stadium theaters. The newer ones are THX auditoriums (though far from the best ones I've ever heard) and you get more consistently decent sound in those theaters. At least there I can understand the dialog, and the surround effect is more convincing. However, for long-awaited blockbusters, I will head over to the Century 21 (an old dome shaped Cinerama theater) for its big screen, even though its sound system is only so-so.
As far as why your system at home sounds better, the answer's pretty simple -- because it can! With a movie theater, the sound system needs to fill a much larger space AND make sure that the sound is halfway decent for the 90% of the patrons not sitting right in the middle of the theater. You're going to have compromises along the way when trying to please this many people.
A home theater only has to play for a smaller sized room, so no need for ultra efficient speakers and tons of amplification. Also, you can optimize the speaker positioning so that the imaging is spot on for your listening position. No need to worry about how it sounds to people in the 19th row seat 20. Listening to a great soundtrack like "Master and Commander" on a properly positioned 5.1 home theater setup, there's simply no way that a movie theater can duplicate the kind of imaging and spatial cues that a good home theater will create with that soundtrack.
Home theaters though do have their tradeoffs as well. For one thing, most small-to-medium sized rooms will create acoustical problems in the bass. Large movie theaters don't have this problem. Also, there are some ambient sounds that a big flank of surround speakers can simply do better than any 5.1 or 7.1 setup can sound off.
Most rooms are not optimally shaped for a home theater. You get doorways, alcoves, bookcases, etc. that are situated for decorating appeal, but not for maximizing acoustical performance. Also, most people have to live life in the rooms where they have their AV equipment, which means that you cannot just put the speakers and subwoofers where the sound is optimal, if that also means blocking an entrance or in a walkway where the kids or pets or drunk roommates run around.