It is possible that another program is changing the modification date of the file. If the file is uses the .eml extension, Windows automatically and continually changes all files, unless you remove \HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\PropertySystem\PropertyHandlers from the windows registry. See http://petersteier.wordpress.com/2011/10/22/windows-indexer-changes-modification-dates-of-eml-files/ for more information.
The sync client has been intentionally limited to sync no deeper than fifty sub-directories, to help prevent memory problems. Unfortunately, it, currently, does not report an error when this occurs. However, a UI notification is planned for a future release of ownCloud.