[cartman1337]

Hopefully this will help troubleshooting this. I tried what someone else suggested and changed my audio output from HDMI to Analog, and after doing that all my MKV files were playing properly. I could even tell that it was coming out of the proper channels. I even downloaded an AC3 test file and verified that when set to Analog, each channel was coming from the proper source. I haven't dug much around to see what the ramifications of making this change, but at least it's usable for now.

The ramifications of doing this is that the audio is not bitstreamed to your receiver/amp. The AC3 sound is decoded by software on your computer, and then streamed precoded to the amp. If you have a decent amp then this will lead to inferior sound quality, as a decent amp will decode the AC3 stream better than a cheap/free software decoder does.

For me the ramifications of switching to Analog output in XBMC is even worse, as I'm somehow unable to get the sound driver to output anything but stereo in analog mode. The sound driver refuses to realize that the amp at the other end of the HDMI cable is capable of outputting more than two channels, and thus defaults to stereo no matter what I do. It's fully capable of bitstreaming, though, and when it does I off course get full surround if the bitstream has more than two channels. As such Analog output is simply not an option. It's digital bitstream or the highway...