This has happened with both AE CS6 and Media Encoder CS6:
I have a Prores file which is 1280 x 720.
When I import it into either AE or Media Encoder they say the file is 640 x 360.
I can view it in 720p on quicktime and FCP7, and the "get info" confirms the file is 1280 x 720.
But the Adobe programs import it as 640 x 360.
If I stretch it to 1280 x 720 the quality suffers, so I can't solve it that way.
The problem disappears if I used Uncompressed video.
Any clues? Is this a compatibility problem? I don't think this happened in CS5. I also recently updated to OS X Mavericks.