Why does rsync update NTFS directories when the source has not changed?

Allow comparison of mod-times with reduced accuracy

It appears in this type of setup where you mount to an NTFS partition you want to ensure you use appropriate parameters such as --modify-window=5 to increase the default value to allow comparison of mod-times with reduced accuracy.

--modify-window 

    When comparing two timestamps, rsync treats the timestamps as
    being equal if they differ by no more than the modify-window value. This 
    is normally 0 (for an exact match), but you may find it useful to set 
    this to a larger value in some situations. In particular, when
    transferring to or from an MS Windows FAT filesystem (which represents               
    times with a 2-second resolution), --modify-window=1 is useful (allowing 
    times to differ by up to 1 second).

Further Resources

• RSYNC
• rsync - man page