My old Def Tech Prosub 80 used to do that on demanding movies. The LotR:FotR DVD in particular is very demanding of subwoofers, a couple of my friends mentioned the same problem you had. In fact, one of them is now considering a getting a new sub becuase of this.
Given the large amount of bass, and the fact that the overall sound level of this particular DVD is higher than normal, if you've never calibrated your sub relative to the other speaker with an SPL Meter or if you intentially run the sub a few db "hot", then it could be that the bass is getting emphasized somewhat more than it should. A lot of people like a little extra boost in the lower bass region, and for many movies it can sound very good, LotR:FotR is one of those movies where the bass is already somewhat emphasized so you don't want to push it too much.
BTW, not to brag but my SVS-20-39PCi had no problems at all with this movie; just clean, smooth, awe-inspiring bass.
