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I don't have an exact answer, but here's what I would try (in case you haven't already).
Delete all of the cache files for a project -- all of them. Start a new project then immediately clean the media cache database. Load an existing project on one system and let Pr regenerate the cache files there. Move the project over to another system and see what happens.
You may also want to try relocating the media cache database via Preferences before loading that existing project, but that's kind of an off-the-wall suggestion.
I don't have better answers because I've never had this problem. I move projects between my RAID-equipped desktop system and the eSata external drive I use for my laptop and Pr doesn't regenerate the cache files. I keep the cache files next to the media.
Could you also tell me how you have things configured in the preferences, e.g. store files with originals or not etc?
What about the write XMP etc?