What type of conflicts? The only way that conflicts can occur that I know of is if shutdown procedures are not followed correctly. (IE: ending task on POS, versus a proper shutdown). Please be more specific.
Also, changes made within System Configuration should not be duplicated at POS -- one or the other.
A great way to remember what to do for shutdown is "D.O.T.S" D=disk in the disk drive, O=open checks; can't have any, T=Terminals all on the logon screen with nothing highlighted, and S=Servers all cashed out. If you follow these rules then shutdown will never be an issue.
What type of changes are you making to the menu most of the time that are not behaving correctly? Price changes? Tranformers? Pop-Ups?
Suchasynic