First off, have you reset the prefs yet or tried .idml on this file? Is it happening with other files, too?
Second, I'm confused about the print. Are you saying it ouotputs differnently from Acrobat than it appears on screen?
Third, have you tried not messing with the settings when you export, then use the optimizer to flatten the PDF?
After a few rounds of testing various things:
I applied a Master Page of None to all the pages - and the pages exported correctly.
I reapplied all the master pages to the various pages as needed. And again it exported incorrectly.
I deleted all the Master Pages - recreated them and reapplied them - and it's all working as normal.
Cause seems to be some sort of corruption with the Master Pages.