There are various technologies to process surround sound, Dolby (Movie, Music, etc.), DTS (Neo 6 and other jazz). It's not really important as a reason why you'd only be getting sound from the left channel, but could explain poor bass management or lack of surrounds.
As far as sound quality of analog vs digital, unless you are pickup interference in your cables, it should be equal quality. Do understand that you'll likely need to manage crossovers and surround processing in your computer as most AVR 7.1 inputs pass the audio straight through to the amp section with little to no processing.