What a mess!!! reading through the original post i would say proper times and everything else was followed to the tee and I have no doubt, everything was activated properly and of most concern would be the primer as over activating can cause this but the time frame is very important as well as humidity and i don't think this is the case at all because even then it will not just come off but takes a good chip to work it loose.
Activating the base actually increases adhesion so we know that had nothing to do with it.
With the above it really only leaves 3 possible causes:
*Primer was sanded when very fresh and then sat to long and closed up cells.
*Waterborne cleaner was still in primer pours and broke adhesion as paint dried.
* first coat of base was dry sprayed or covered from over-spray if other parts of car were painted first.
My best guess would be primer closed up but the big flakes are acting like trapped cleaner and that confuses me, so I wonder could it be a combination of 1 and two 2? It kind of sounds like it.
You mise well bite the bullet and lay some two inch tape on the other panels and snatch off to see if you have adhesion in those spots.
If you do, that kind of points to 1+2 on the doors.
This is the best I can come up with but let me know and let me know what you need to finish doors up, if you are running short.