Keep in mind that "lots" of bass isn't the same as "deep" bass.
If your system isn't calibrated, your sub probably has a peak around 40Hz, which gives most people the "wow" factor. If your system is calibrated to flat, the sound is very different.
I used to get "big" sound on the Jericho track with the music when the rocket launchers were turning. Impressive, but not "right." EQ'd, the music is even across the spectrum, and the big "boom" is saved for the landing of the rocket, as you would expect.
See some of the illustrations here:
The New Master List of BASS in Movies with Frequency Charts
I keep bringing this up, but I think it's important, re: Pulse:
The "thump, thump, thump" is cool, but if you can't hear her heavy breathing, feet dragging on the floor, and the rustle of paper as she turns the corner, your bass is drowning out the more important effects of the scene. And of anything else you may listen to. Which is why measurement and EQ are so important.
Choppy play is usually a mismatch between player and brand of disc. I use an HTPC, so I'm afraid I can't offer any specific advice. You may want to look on a thread dedicated to your player; I'm sure people there would have recommendations.