Hey guys,
I’m learning that Plural Eyes can’t really handle MTS files. I used MPEG stream clip and converted my MTS files to quicktime. Then, from within Plural eyes, I started a new sync and had success. THe drawback is that if you have MTS files, it is probably because they are very long in duration. When streamclip converts them to quicktime they become huge! I had a 4 GB MTS file that turned into a 45GB quicktime. Pluraleyes can work with them, but now my hard drive is just about out of space.
If you are in a bind, however, this should work. Download the stream clip application if you don’t have it, it is free and really useful. Adobe Media Encoder should be able to do batch conversions as well.