I think cg might of been onto something with room acoustics. The biggest bass issues anybody has are caused more by the room than anything else. I'll suggest two things that could help...

1) For a quick, and cheaper, start, you can try out the "Subdude", aka "GRAMMA", platform as made by Auralex. For $60, this wonder of wood and acoustical foam isolates your subwoofer from the floor, reducing room interaction and boominess. That's not just type, I own one and that's exactly what it did for me. I'm not saying it corrects all bass problems but it's certainly a start.

2) Look into getting, or making, some kind of bass traps for your room. This doesn't mean covering your room in egg crates or putting up a lot of curtains but actually investing in a full-range absorber of some type. For me, the best advice I've seen seems to be coming from Ethan Winer and his site:

www.realtraps.com

As an alternative, you can also find a ton of acoustical information on the Auralex website.

www.auralex.com

From your post, it sounds like you have some sort of test equipment. If you're serious enough to get something like that, investing in acoustical treatment should be a very small but very important step.

Good luck...

P.S. You're more likely to get replies if you list what equipment you're using.