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.

And all consumer facing audio messes around with frequency response.

To put it another way “sounding good” is a question on the audiophile spectrum where people demagnetize compact disks and can hear the difference of premium HDMI cables.

youtube - the audio on youtube is.. not.. quality. i had a friend who used them as best-audio-compression-ever :) maybe, Opposite of all above, It is possible that now you are hearing their garbage that was unheardable before.

games - similar.. it's not an audiofile genre.

Get some proper sound out (e.g. flac or .ape or something) of something that you know how it sounds (piano? voice? some old electronic stuff?) hopeing it's not over-engineered at studio.. and check that. Better, multiple things ..