this is caused by a fairly complex problem that has been discussed here: http://email@example.com/msg09439.html
the short explanation is that files originally stored as binary (with crs) in the repository are now being handled as text, so git checksums those files (without crs) and they "look" modified because the checksums don't match.
unfortunately, git does not know whether a file is stored in text or binary mode in the repository (it's not in the git file format specification), so this problem can't be fixed efficiently. the expectation is that people should "fix" their repositories by re-committing those files as text, since they should never have been stored as binary in the first place.
another way to deal with the problem, if you don't need git to convert the line endings for those files, is to set up your linux repository to treat those files as binary (e.g. add a " binary" line to your ".gitattributes" file).
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