John, its a good idea in CS5 to render out any dynamically linked clips in the PrP timeline, in AE.
By that I mean open up the AE comp, render out the sequence, then import it into PrP. If you load it into the source monitor, you can then highlight the existing (same) AE comp clip on the PrP timeline, then right click, and choose REPLACE WITH CLIP IN SOURCE WINDOW. I do this process all the time just before creating a master because AE renders stuff faster then PrP AND it avoids certain gotchas with AE comps in PrP timelines.
Dynamic links are great for fiddling around and getting things the way you want, but render and export from AE then import into PrP and replace on the timeline.
I hope this addresses your issue.
Clear? 😀
Tom Daigon
Avid DS / PrP / After Effects Editor
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