Help. After re-installing Logic...it gets the clips wrong

Hey. I've just re-installed Logic.
I've just gone to open up a project I was working on previously and it says that it couldnt locate one of the audio files. No bother, I told it where to point to.
The problem is that it has put the wrong regions in the wrong places, and has forgotten some of the edits. It's only happend to one audio file as well....
Any ideas of causes and fixes.. I don't really want to go back and re-edit the audio file...

Yh I checked the last backup file and it happend the same way...

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