Using the RoleSync utility to schedule Active Directory Group assign/update application users to a System Role sets Site Security to 'All records'. This disregards any site security assigned.
Using the Synchronize button within the System Role's Group tab updates the users site security correctly. The client though would like to schedule the udpates in the back-end using RoleSync and Task Scheduler instead of manually going into each System Role's Group tab and clicking Synchronize.
Download and install the latest version and patch, if applicable.