Cinema is set at 25fps my output is a 1280x720 at also 25 fps with square pixels. I exported as a TGA sequence with an alpha and straight alpha channel and the 8 bit Dither is on (must of been the default)
Anti - Aliasing is 'best' and set to animation. I converted the TGA sequence in AE as a QT at 25 fps as RGB+Alpha.
When played in FCP (after rendering the timeline) I get jerky playback it looks like some frames are not there or the frames rate had been set wrong.
Might be that your files are a little to big for your computer to play back at full res. Try lowering the quility of your timeline.
If that does not help check your AE project RAM preview see how the playback is there.