Perhaps you are not enabling Track Automation. That could make a gigantic difference.
Some tracks could be set to output directly to your sound card/interface instead of to Master. When I create new tracks, they default to VS-700 MAIN (my primary audio output) but they used to default to Master, which is the documented and correct behavior. I don't know if this is a consistent bug or related to some project corruption, but a user could also do it accidentally.
Similar to the above, you could have tracks routed to a bus (mix or effect) that is not going to Master.
Also, if you do not check Enable Live Output, you can hear some non-recorded or non-frozen tracks in your mix that will not be exported to the WAV/MP3.
Could be other stuff, but that comes to mind.