Most mulitchannel cards have a tone test which allows you to certify that the speakers are correctly plugged in and working
If that is the case, play any troublesome file and in ac3filter config, make sure the output type is 5.1 (of course your file must contain 5.1 audio track) and the channels appear rendered in the output meter
Other than that, all I can think of is updating your soundcard drivers to the latest ones available :?
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