HELP! Transitions are jerky in final export -- faint green line?

Hi all--
I'm really confused about what's going on with a project. I'm working in DVCPRO HD 720P 24
With a 23.98 framerate and compressor setting at DVCPRO HD 720P 60.
All of my footage looks fine, but I have a number of QT files that I created in AE that, while they
look just fine in the timeline, the transitions in and out are really stuttery. The wierd thing is that this stuttering doesn't show up while playing the clip on the timeline, but does when I view the final exported QT file of the whole piece. The AE graphics were created in a 23.98 comp and exported using the DVCPRO HD 720P 60 compressor setting. Usually this all works out fine, but
I can't wrap my head around why this time the final piece won't export out of FCP without these jerky points occuring with every transition in and out of a motion graphic sequence.
There is a very faint green line over every one of the transitions--one that Im really not familiar with. I know this means something, but I don't know what?

Any thoughts would be great as I'm on deadline and I can't deliver the final like this...

Thanks!!

It means you have to render. Go to your render settings under Sequence > Render All > and put a checkmark next to 'full'. Then go to Sequence > Render All > Both. This will fully render out your timeline and should remove the bumps.

Thanks--

Yeah I've checked full render (I've tried them all, in fact) and then select "render both:" it does a render cycle but the green line then turns to blue. In the timeline these transition points continue to look fine but when I export
(current settings) I end up with the same thing. It's really weird. Is there something I'm missing in the render command?
Thanks-