My Restore Points statrted to disappear after I upgraded Defraggler to 108 version. I uninstalled this version and reinstalled Defraggler 101, and ran (after creating manual Restore Points), the Restore Points remained.
I am running Vista 64 Ultimate. I also tested this situation with Windows 7 Besta which I am running on Virtual PC, exactly same result. IN MY CASE, the issue has nothing to do with CCleaner which I also use (latest version) or Recylce Bin.
Hope this helps, any feedback would be appreciated.
Mike