InDesign keep telling me I have missing links.

Hi all,
We recently did some server switching at work and let me say upfront this is not one of the "How do I update thousands of links?" questions. I have already combed through those with mixed results. Anyhow, after moving everything and opening ID documents from the new location, it tells me the links are missing yet when I check the paths they are correct (for the new location, as if ID figured it out). Upon opening, if I look really quickly at the links panel, the red question marks are there and it seems to quickly correct itself. Again, the updated link paths are correct. My problem is, it does this every single time we open the same document. It always tells me links are missing and automatically fixes them. I have tried saving the ID file under a new name with the same results. I have tried "Save as" under the same name with the same results.
Anyone ever run into this and if so, is there a way to prevent it? It is somewhat annoying to have to click OK on a pop up every time I open a document when I know the links have been updated and are pointing to the right source.
Thanks to anyone with input.

Thanks for the responses but perhaps a little of more information is necessary, ....
It is not just one file, it is all files after the server switch.
We have two users on ID CS5 and I am on ID CS4, both ID CS5 users experience the same problem and when they export it to .idml so I can get at it, same thing.
These files were all converted from Pagemaker to ID.
Again, the path appears to be correct (after ID self-corrects) as an end result but it keeps asking every time the file is opened (regardless of the ID CS4 or ID CS5 user).
I'll try converting a single ID CS4 file on my machine tomorrow to .idml and then re-opening to eliminate some variables and see what happens. Will post results.

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