It's a Bose.
I'm sure if you use your search function for the forums you can find answers for this, but the general consensus is "Bose is all midrange, sucks at highs and sucks at lows".
Your center probably sounds hollow because it is. If you were to DIY build your acoustimass system with identical drivers, you would end up paying less than $500 for all of it.
Bose is marketing and name brand identity - driven by marketing.
You could save sunk $1200 into an Atlantic, Energy, Deftech, or CSW set of speakers and gotten more versatility, deeper, richer bass, and well defined highs...and probably been 100x happier with the final product.
If you really want to clean it up, I'd sell the bose system (they have good resale value) and replace with something (almost anything) else.
OR tell us what Onkyo you are using and what listening mode you listen in. Also, did you run Audyssey in 6 listening positions? What did it calibrate everything to?