InDesign Server 5.5 Missing Links

I'm getting missing link errors in the log when InDesign Server opens files. The missing links reported are for xml files and snippets. Opening the document and looking in the links pallette shows no missing links. I tried using AppleScript to see if I could access these links but they are not there. I can find the links if I open the document in a text editor so I know they are actually there but I cannot seem to find a way to get rid of them. Any suggestions would be great. Thanks.
Has any one else seen this problem?
Is there some way to "clean" the file? ( I already tried doing a save as on the files. )

I encounter the same problem with InDesign Server CS6: I get warning messages about missing snippets. This does not prevent to generate PDF's successfully (with madeToPrint server), but I would like to understand…
Any idea?

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