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No idea. This may be a specific problem with the camera model and the files it generates...
You haven't explained your workflow very clearly. What file format are you using with alpha channel when you return to PPro from AE? As far as I'm aware, AVCHD doesn't support embedded alpha channels.
Personally, I'd convert all files for AE into lossless quicktime files before you do any work on them.
I am shooting in 1440x1080 60i to create the AVCHD file.
Would it be best them to take all my AVCHD clips and convert them to quicktime files with Adobe Media Encoder?
Would you choose the animation codec? There are a few other options I am not sure on but have stumbled through.
I set frame rate in media encoder to 29.97, progressive (since it was shot at 60i does that mean I should choose interaced? Progressive seems to work OK).
Codec settings offer 8, 16, or 32 bit. I don't know what to choose there.
For aspect ratio I chose HD Anamorphic (should I choose square pixels). The reason I chose anamorphic is that 1440/1080 = 1.333 and that was the only setting with that aspect ratio.
Thanks again for your help. I'm new to a lot of this (obviously)...