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What are you using to change the mts to pro res 422? Just use log and transfer through FCP?
I had this exact same problem with my GH2 footage and it was the program I was using to change to pro res 422 (ClipWrap), for some reason it was not doing it properly, so then I used MPEG Streamclip.
Made the switch to Cinematools eh Evan??
mpegstreamclip does all, by the way.
Update: Ran the files i got from clipwrap (which were 1080p60) and put them through mpeg streamclip (as 1080p60 again) and they worked in cinema tools. Kind of annoying but hey, it works.