the Windows/WMC audio settings are in play if you have no external codecs/filters/decoders installed on your system. once you do install a "codec pack" you can set it to take precedence over the baked in Windows settings.
on my system I have the Shark007 codec pack installed and I have audio routed through the ffdshow decoder. I set it up this way because I have an older 5.1 system without HDMI in and HD audio decoding abilities.
by using ffdshow I can have it re-encode HD audio or multichannel AAC audio to a 5.1 Dolby Digital mix. It works with FM radio too for instance - instead of a 2.0 channel PCM signal going to my receiver I can manipulate it to send a 3.1 channel Dolby Digital mix so that it plays across all three front speakers.
From my perspective you can solve your problem one of two ways:
1) by having the playback system set up for 2 channel, but setting up your sound card settings to use all four speakers
2) by using an external filter like ffdshow (AC3 filter may work too, its been a long time since I've used it) to decode your 2.0, 5.1, and 7.1 audio tracks into 4 channels that will play nice with your speakers
this is the setting you would manipulate in ffdshow:
edit, I see you've found that too.
what exactly did you download and install?
also, what kind of audio system do you have and how is it connected to your pc?