Short version of what worked for me:
.WAV or .MP3 Mix Downs did not sound the same as the project itself.
After about 15 different Mix Down tests I determined the difference was between "Use Selection" & just mixing down the whole project.
Regardless of MP3 or WAV the "Use Selection" was not Mixing Down the audio correctly.
I'd tried basically everything I could find posted on the forums, this worked for me and pointed out a clear difference consistently. Whether my OS, settings or hardware is somehow still to blame I'm not sure.
Part of what made this frustrating was that I'd previously mixed down to either format without issue, but I could not figure out what the difference was or what I'd changed. Well the difference was that I wanted to cut ~40 seconds off the front end of this track, and was using Use Selection to do it.
I had one specific section of the track where (2) short, close together samples were having an odd delay added between each other that was very noticeable. It was pretty easy to spot a bad mix down each time based on that.