I've looked all over the web for threads on the subject of FTM 2012 and its ability to import native Legacy 6 files. There are many such threads and the consensus is that it is a dog. I totally agree. The first time I tried it I lost my thousand or so images when it synced with the online tree. I tried again and manage to get those back but then realised that all my notes were either misplaced or missing. Then to make matters worse I discovered what many people online have complained about - the import file connects parents to children incorrectly and loses connections to the real parents so badly that the entire family has to be reconnected manually. If this only happened once or twice I would say it was worth the trouble to have a family tree file that can sync with the online version. But when I realised there were dozens if not hundreds of such errors in the file I decided it was a waste of time to try and remove them all and I had to erase the online tree so that those viewing it would not mistake these relationships as real.
So long story shore, importing to FTM 2012 from Legacy 6 is not a wise thing to do. Maybe with the next bug fix aka release?