That sounds like Room Modes to me, or a poorly designed enclosure, I have 4 subs in a small room 2 sealed and 2 huge vented/Sealed sonotubes and the they sounded very similar to what you were explaining (some music good others too much boom) it didn't matter if the Port was closed or open, same problem. Then I added a Behringer Feedback Destroyer and Viola, everything is sooo much better and my SPL measurements back it up. I'm within +/-3db's from 15Hz to 80Hz, and now when I close the port (different correction values) it sounds very tight, although I still think the vented version sounded smoother, and I actually prefer the Vented sound to the Sealed for most Music and all Movies.