We just upgraded to InDesign 5.5 and we noticed something funny. We're working on a NAS server that holds files that eveybody shares. When we link to one of the files on the NAS, everything is fine until we save the document. Then the links panel shows that the link has been modified and needs to be updated. We moved the file to the user's desktop and got the same problem.
Do you run Suitcase? If so, install the latest patch from Exensis.
Just did and it solved the problem. Weird, I don't see the connexion between suitcase and the link palette.
Don't have a clue why, but one of the previous suitcase updates was responsible...