I added /A-:SH to my copy script and the system and hidden attributes were cleared at the end of the copy.
robocopy d:\ j:\d\ /MIR /A-:SH /XD '$RECYCLE.BIN' 'System Volume Information'
I found this fix here:
http://forums.overclockers.co.uk/showpost.php?p=12824596&postcount=3