To the best of m y knowledge the only way what you describe can happen is if the files were opened and saved in the newer version. How did you verify this is not the case? I would suggest using the script at Adobe Forums: [Ann] Identify Your InDesign File
This was confirmed by restoring old backups of the files which were saved with ID5.0 prior to the install of ID5.5 on this system. Also confirmed that the test files had last modified dates from many months prior to the 5.5 install taking place. There are no other users here who use ID5.5 (or later versions) so it's extraordinarily unlikely that these files could have been modified by CS5.5 in any other way. I can try running the script above and do some testing.
CS5 and CS5.5 are totally separate and do not interfere with each other.
You are not the first to claim that a file could not have possibly been opened and saved in a later version and almost every single one of those instances it was shown to have to have happened anyway.
If you’d care to post a few of the files in a dropbox folder and provide a link I’ll be happy to check.