Dynamic link to After Effects problem

My computer crashed a little while ago, and we had to reload the system, but no data was lost.
The project i am working on, has every single shot dynamicly linked to After Effects.
The links held up fine, but there is one problem, about 10 shots have some how recut them selves, and or have been shortend. The funny thing is, is that some how the audio still matches up. I cant seem to figure out how to solve this problem.
Any help at all would be greatly appreciated,
-Izzy

Just an update:
With disc utilities I repaired the permissions.
I reinstalled cs5 production premium.
I updated it to the actual version (flash occured an error, but the other ones were fine)
I opend the project: no links to most of the media.
I relinkt all media - except the dynamic links to After Effects. That just doesn't work.
I saved the project on a different drive with a different name.
Opend the new project and - again - most of the files didn't link again! Missing more than 10.000 links to jpegs, psds, mxfs.
I opend the new and the old project on another mac - same results.
I think, repairing permissions with disc utility doesn't affect Adobe's software (Apple says that some 3rd Party Applicaton might not be affected.)
I found a workflow for repairing permissions in the case of updating-failure, but I didn't try that, as I don't want to make things worse.
Is there a way to repair CS5 permissions "internal"?
Thanks in advance,
Philipp

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