Dude if you spend $10,000 dollars on a computer, you should absolutely expect it to be perfect, I don't blame you one bit. The same can be said for the cabbage you gave for your speaker system, it should be perfect also. Never settle for less when you're paying for the best.
One other point I'll make, when listening to 5.1 the bass signal sent to my EP800 is not nearly as strong as it is in 2.1 audio mode. That's probably why my 'volume' knob is set at 50% instead of 20 - 30%. If I listened in 2.1 I probably would turn it down some since it's so over powering. So try this real fast, set your receiver to stereo and see if it makes any difference in the bass output. If not, then I guess we'll have to wait and see what the pro's say.
Oh and don't worry, my EP800 reached me in anything but perfect condition. I've been hearing a lot of complaints about Axiom subs as of late, a lot of similar issues occuring with the new models. I'm thinking the new amp design may have some bugs to work out of it yet. My 800 for instance had a bad amp that damaged (my theory anyway) both of my speakers. I have since swapped out the amp and one of the woofers, and now I'm waiting on getting my other replacement woofer. For now anyhow the music sounds absolutely fantastic! But movies drive it into distortion. Sounds like exactly the opposite problem as you are having. Rest assured, if there is a problem with your EP500, Axiom will take great care of you!
