Sadly, the global sort and many of the other "features" introduced in 2014 are really fixes that should have been released in patches to shore up all that didn't work when TreeSync was introduced. For new users, I'd recommend starting then with 2014. For existing users, I'd recommend paying the money to upgrade, because you're using a buggy piece of software from a company that makes you pay for bug fixes, but there is no way else to get them, and some of the bugs in 2012 that are fixed in 2014 make it worth the expenditure.
Question: you said you exported via GEDCOM to RootMagic 6. Did you use the flagged errors there to correct your FTM file? Or did you make the corrections in RootMagic and then export back to FTM via GEDCOM? It's hard to believe that you wouldn't lose or effectively corrupt data by doing the latter.