I suppose you could offer more details...
Starting with Ubuntu version and how your audio connections are done. There are many threads about audio problems in ubuntuforums.org that can help you as well. That weird thing you mention has happened to me as well, but with the sub, like u pick another and then the sub starts working and I pick back the one I had and it still is working, and since is like that.. I would think is more related to Ubuntu than with XBMC.
I dont know that Acer model, but I'm guessing you are connecting it to your Denon with an HDMI cable and then back to your plasma the same way. Far as I know, HDMI audio only works with some brands, like ATI and I think recently nvidia, but never heard if intel is too, but I guess somehow is working for you (unless you're connecting your audio separately with a cable with headphone plugs on both sides).
Also, I remember hearing somewhere that when using the optical/digital (SPDIF?) or HDMI... the audio in the system is set as 2 channel and then your receiver interprets the signal and process as DD5.1 or whatever it has, which could relate to what you say in the end.
Anyways, you are missing details and without them... the real gurus can't help you. But do check those audio threads in forums as well, like this one:
http://ubuntuforums.org/showthread.php?t=1307019
Hummm, another thing.... in my system.... whenever I log in... I have to reduce the volume to zero and then back up to whatever level I want it to, so that all speakers work as normal. I have 5.1 sound and I have all my speakers volume set at 100% and I just control the master. If I dont reduce the volume to zero... many times happens that the volume in each channel is set to 70% and even the sub is lower than that. After I do the trick... all speakers are set to 100%.
When Im going to use XBMC... after I reduce to zero... I go all the way up to 97%.
Hope this helps...
ELP