Sounds like horizontal pixilation try this…
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Select a piece of footage from FCP (I take it these will be 1080i50/60 Quicktimes).
Open it into Quicktime Pro (I hope you have this too !!?)
Open the properties for that movie.
Select ‘Video Track’
Click on the ‘Visual Settings’ tab.
Uncheck off ‘Preserve Aspect Ratio’
Change the ‘Scaled Size’ from 1920*1080 to 1440*1080.
Hit the save keyboard command (Command S for Apples)
All the above will do nothing to the file other than change the ‘header’ no data will be lost.
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Now bring this footage into AE and make a new 1920*1080 comp with square pixels.
Should solve your problem.