There is likely nothing lacking in your sub. The Audyssey automated speaker setup should have set the crossover and the levels for you but you can tweak them in on-screen receiver settings.
The most likely culprit is the placement of your sub. Try moving it laterally along the front wall and experiment with distance it sits in front of that wall. Just small changes in location can make drastic changes in sound. Individual room acoustics can cancel out some of the bass frequencies if it happens to be in the wrong location (they can also artificially reinforce the frequencies giving you boomy, muddled bass). After you find a new location it would be wise to run the Audyssey setup again to make sure the levels are appropriate.
I recently upgraded from a Logictech Z2300 (meant for PC use) to an Onkyo 9100THX. I set up everything using the Audigy microphone method. When playing through any non-hdmi source, bass is underwhelming. I am outputing music through optical and is doesnt base lacks the impact it had using a headphone jack to my old pc speakers. I also tried using the red and white rca cables and got the same results. I can't seem to find crossover settings on this receiver. I can find settings that allow me to adjust +- db for ~5 different frequencies for each speaker, but I thought crossover is where you set the frequency that each speaker kicks in at? It seems to be pushing all but the lowest of the bass to the front and satellites, which does not sound good.
I hear the Onkyo receiver is a decent one, so I would be surprised if it didn't have crossover control. Thanks in advance!