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We have files that should be executable, and are happily executable in git, but then editing and committing the file from Eclipse on Windows results in the file mode being changed to remove executability.
This happens regardless of whether core.filemode is set to true or false.
Basically egit seems to be too naive for our purposes (breaking file permissions is the problem, but it also doesn’t seem to support git-svn) so we’re using msysgit instead – we have to manually refresh in Eclipse after switching branches etc, but that’s a small enough sacrifice compared to it breaking our code.