Thanks for the replies guys. 
@dotVIBE:
1. Resetting your AVR sucks. It shouldn't be necessary and it's a pain to set it up again. That said, the newer stuff are pretty much computers in their own right, and it's not surprising that a reset now and again is in order. It's something I live with with my AVP. Check with your dealer whether he can load the newest firmware for you. There actually aren't that many options but before I reset, I will make a note of all my current settings. I don't think firmware can be upgraded on this model Onkyo [link].
2. Don't run Audessy when you bi-amp? Do you bi-amp? or bi-wire? if you bi-amp ( couldn't imagine why you would want to) just disconnect the LBR and RBR cables from your amp and put the jumpers back on your towers' speaker binding posts. run audessy, and then fix it back like it was. Well I only have a 100Wx7 AV Receiver and RTi A7 speakers. So to pump them up I am bi-amping, which is how the installer set them up. From what I can gather the front speakers are now running at 160Wx2 per speaker @ 6 Ohm.
3. As far as sound settings are concerned, stay away from the DSP modes (Hall, symphony, whatever). they are kak. THX anything also messes with the sound. But you can always try it and see if you prefer it. The main ones I use are PLIIx Movie when I watch stereo tv and want to matrix it up to 5.1 sound, PLIIx Music or All channel Stereo when I have a party and want music to play through all the speakers. Your Onkyo, like all current AVR's has way to many sound modes. I'd stick to the "TV" mode and let it auto select Dolby or DTS when you pop in a movie. Yeah I'm gonna try set all the sources to Direct and give the listening modes a break because I'm probably too used to them now
4. Maybe check your BDP or whatever and make sure you didn't lower the volume on it. I've got a PS3 which I hardly use. Almost all my video comes from my Pace TDS850 HD PVR - recorded 720p content. No real settings there so it's only the Onkyo
5. Not sure what you can do about optical ports not fitting nice. not much i suppose. My personal preference is not to use optical at all. Too prone to jitter. Digital coax has always worked for me. Since the PS3 clicks in, as did my previous DA-5500ES Sony, why would the Onkyo be different? It's like they using a poor quality optical jack? Nevertheless, the HD PVR and PS3 only have one of each output. Think the PVR is digital coax and the PS3 is optical.
@Daniel: I don't really understand Intellivolume so need to learn more about this.
