There are (at least) two different problems being referred to in this thread.
Problem #1) The Realtek HD drivers for Windows 7 -- at least the 64-bit version -- for some reason default to a 5.1 speaker setup having "side" speakers instead of "rear" speakers, but the driver defaults to the third speaker port being mapped to the "rear" speakers. This means that if you set it to 5.1 speakers and plug 5.1 analog outputs into the default ports on the MB, the rear speakers will not be getting any sound.
To fix that, just go into the "Realtek HD Audio Manager" (under Control Panel) and change the jack where the rear surrounds are plugged in from "Rear Speaker Out" to "Side Speaker Out". Changing the speaker setting to 7.1 will also enable them as rear speakers, but this may sound weird if applications like games or DVD/Blu-Ray movies attempt to play true 7.1 audio, since then the side speakers will be missing.
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To be fair, the AC97 audio standard that PC's use defines the first extra pair of speakers as side speakers, not rear speakers. HT setups that use Dolby/DTS audio define those same speakers as rear speakers, however, which can really mess up playback when trying to play decoded DD/DTS audio on a PC...As said, you CAN enable 7.1 and toy with the speaker settings, which ""fixes" the problem.
As for the second problem, if you play 2.0 audio files, it will output only to the first two speakers. This is normal, and I find most upmixing on 2.0 audio to be subpar, to say the least.