I originally thought that RSync was missing data during the copy operation. I have now discovered that the issue is NTFS permissions.
Even though I am running the RSync server as a domain administrator and the copy operation as the same domain administrator the NTFS permissions on the files are causing issues.
Once copied some of the files either get their permissions changed or blow so that the next time the RSync operation runs it is not able to change or delete the remote files anymore.
I have the CYGWIN environmental variable on the server with the value of "nontsec" and thought that was the fix. Is there a way to make sure the NTFS file permissions are not changed on the destination so they are the same as the source? Both source and destination are 2003 servers.
Running a command after the fact to set permissions may not be an option as the data set is 1.6TB and millions of files.
Any help would be appreciated.