Actually that wasn’t it. I had tried that. The makes sense though.
What I figured out is that my export settings from final cut had changed. It was coming over 1280 x 720 with the wrong pixel aspect ratio which AE was trying to fix i think. Also I think the preset was making it 29.97 which is not how the footage was captured. I actually think that was the main problem.
My settings for export from final cut ended up being:
frame size HD 960 x 720 (16×9)
pixel aspect ratio: HD 960×720
editing timebase: 59.94
timecode rate: same as editing timebase
compressor: animation
quality: 100%
settings from AE:
interpret footage:
frame rate: 59.94
separate fields: off
pixel ration: square
comp settings:
preset HDTV 1280×720
pixel ratio: square
frame rate: 59.94
thanks!