I have some files that are .dat data files and some are .exe files which I renamed to .ex. But when rsync copies the files to the destination folder, it also renames them to "File.dat.ex" and "File.ex.exe" which causes synchronization issues on multiple machines. You can recreate this by rename any .exe file to .ex and run rsync on it.
I am using rsync from cwRsync on Windows 7 and I do not believe this bug have been fixed as I have searched bugzilla and changelogs to the newer versions.
please provide the output of a directory listing on the source and on the destination, it`s hard to believe that rsync renames files that way on transfer. are you sure you have not been misled by windows filename extension hiding in windows explorer?