This has happened a couple times now, where I'm using Premiere Pro CS5 and After Effects CS5 with Dynamic Link, and everything will be working fine until suddenly Premiere Pro decides to render the linked compositions differently than AE. I can still see the composition working just like it should in AE, but in PrPro it's like the timing's off or something. I've attached an example.
This is what it looks like when exported directly from After Effects:
And this is the one clip exported from Premiere Pro through Dynamic Link:
Look at the gunshot for the guy in the left foreground just before the 1 second mark.
In the past I've managed to fix it by opening it up in CS5.5 on a friend's computer and converting the project to the newer format. Also, I managed to get it to work once by simply deleting all the layers in After Effects and then Edit > Undoing it. But that only worked once. Any ideas what may be causing this issue and how to fix it? This has happened to me in past projects as well.
Actually, you posted not the best example, 'cos I'm unable to catch any differences...
However, some Adobe Dynamic Link bugs found (have a look at this thread for example: http://forums.adobe.com/thread/866991?tstart=30) let me guess you need to re-render 'Entire Work Area', not just 'Effects in Work Area'.
Select your composition in Pr Pro sequence and just copy it into clipboard (Ctrl + C / Cmd + C) - now you are aloowed to 'Render Entire Work Area'...