It appears there's a render/playback issue when using Digital Juice Jumpbacks with the latest update to Ae. I recently worked on a project that used a Jumpback and it would have taken 25 hours to render when previous renders on earlier versions of Ae only took 19 minutes. The work around I used was importing the the Jumpback into another editing program, export out as a .mov file and re-import into Ae. This has happened it the past but was corrected, will it be corrected on the next update?
There's nothing unique about Jumpbacks as far as I know. What format and codec are the ones you're having trouble with?
Also, double-check that your composition hasn't inadvertently been set to use the ray-traced renderer.
Are you still facing this problem? If not, let us know how you solved it. If so, please let us know so we can assist you further.