Are you running an SQL DB?
If utilizing MS-SQL for the SEPM database, it is preferable to run this on a physical machine (as opposed to a virtual machine).
- This will ensure less chance of Disk I/O and other resource bottlenecks
http://www.symantec.com/business/support/index?page=content&id=TECH92051&actp=search&viewlocale=en_US&searchid=1294862627142