I've been using Ubuntu for some time now but only after I got a new 5.1 speaker system, has this began to create a problem.
I am using an
ASRock N68C-GS UCC Motherboard with on-board audio and faced a similar issue on Windows 7. The drivers that came with the motherboard only supported stereo sound, as the rear jacks are only Speakers, Line-in and Mic. I somehow managed to download and install a different set of drivers from VIA audio.
I could find a solution to this on Ubuntu however. I'm currently running a Daily Build of 13.04.
In the sound setting, selecting Analogue Surround 5.1 Output changes nothing as the 2 other jack are still recognised and rear mic and line-in in the input section.