ITunes has a "sound enhancer" that kills the center etc. In preferences. Along with the equalizer. And even beyond those settings, ITunes and Quicktime player can still sound different. Quicktime player is usually accurate.
The rumors about bounce to disk sounding any different from record to disk are 100% false on their face. You can be certain that even if someone claims they are "famous"
that their opinions can be discounted if they claim this. Nulling tests have demonstrated there is no difference.
Another lingering issue was automation sounding different and this too has never been demonstrated.
Anyway most likely your files are fine and your systems and apps are screwed up.