that seems most likely to be the root cause of the change you're noticing.
if the source audio is 2-channel, do you have it only play on the L & R speakers, or is it getting output to all 6 speakers? that sort of upmixing needs careful tuning, if it's not done well it may sound "muddy" due to the slightly different delays in sound from each speaker reaching your ears.
if you want to isolate it as a controlled variable, hook up only your L & R speakers, play a test track, and see if the perceived quality degradation is still there.
This seems like a good candidate for an explanation. Stereo to 5.1 upmixing can be done on many different ways, and is likely to e different on different brands of sound cards.
Both in levels of sophistication but also just different options/choices, and one might have a preference for on or the other.
that seems most likely to be the root cause of the change you're noticing.
if the source audio is 2-channel, do you have it only play on the L & R speakers, or is it getting output to all 6 speakers? that sort of upmixing needs careful tuning, if it's not done well it may sound "muddy" due to the slightly different delays in sound from each speaker reaching your ears.
if you want to isolate it as a controlled variable, hook up only your L & R speakers, play a test track, and see if the perceived quality degradation is still there.