How do you know the BESMgmt database is getting slammed? Are you getting any errors in either servers event logs? Perhaps the SQL logs?
What version of SQL & Service Pack are you running?
Was the database ever MSDE or has it always lived on a remote SQL server?
Are there other databases on the SQL server you're using?
A full slow sync backup & restore occurs when you upgrade from 4.0 to 4.1
Make sure you verified everything listed in KB Article 05217 - Checklist for upgrading BlackBerry Enterprise Server 4.0 to BlackBerry Enterprise Server 4.1