I have had the problem with duplicates created by FTM/Ancestry sync when my tree somehow got corrupted. I didn't have as many as you, but I did have a bunch who were in exactly 4 times. I had to locate them (via the duplicates report) and go through and delete.
FTM worked well for me for about 6 weeks since the last sync problem I had, then last night got a sync error and it won't sync now at all without the error.
I also use Ancestry.com as my primary tree and use FTM only for backup and for the reports.
I've sent in a trouble ticket on this error. The last few times I have sent in trouble tickets, I always had to re-download my entire tree to fix the problem, then it works for while until "something" causes it to not be able to sync anymore. It's very annoying to still have such issues.