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I am running a trial with version 11.0.1.5 (64bit). The source system is Windows 2003 with all sorts of NTFS permissions based upon AD users and groups. The target system is Windows 2012 R2 Data Center. Both systems are in the same AD forest, but they are in different OU's.
For my first test I copies a 90GB folder for testing with our IT group. I noticed that none of the NTFS permissions from the source system copied down. I did chose "Copy NTFS permissions" on the Copy Option tab. Is there something else I should select?

BestSync only copys NTFS permissions between local NTFS folders.
If the two folders are in different PCs (NAS), BestSync will ignore the copying NTFS permissions setting.
And the USER ID of different OSs are different, the NTFS permissions may not be copied correctly.