Had a quick glance at the manual
http://www.intl.onkyo.com/downloads/...5_manual_e.pdf
a few things spring to mind. On my Onkyo you can tell it what speakers you have connected, if any, to each set of terminals. That means, None, Small or Large. None should be obvious. Small rolls off the bass end a lot more than Large.
So first thing I would check is what the settings are for each speaker. See the Advanced Setup section of the manual for details. There is also a level calibration option in the settings. This sends a test tone to each speaker in turn which allows you to equalise the volume of all the speakers and also test they are actually working!
The next thing to check is that you are not using a stereo mode which may well mute the rear speakers. And finally check the A/B speaker mode A only should be on for full 5.1 operation.
Once you have the speaker set-up sorted experiment with some of the sound settings. I found with my Onkyo amp that some of the room eq settings could make it sound pretty naff. My amp has an auto calibration mode that uses a plug in mic to set up the speakers itself, not sure if yours has this option? But I found I still had to tweak it to make it sound decent.
Also some of the options for things like Dolby ProLogic can affect the sound quality. On my amp it has settings for Movie and Music and I found the Movie options sounded really poor compared to the Music options for example.
Trouble is there are so many tweaks on the thing that it is relatively easy to get it all screwed up! Takes some perseverance to go through all the various settings and get it sounding right.