Moved to ePO for better support.
You may want to check out the CPU usage on that particular instance it is using in SQL.
I am having the same issue currently from an upgrade from 4.6.6 to 4.6.7 and it is under investigation by McAfee.
In my occassion it is a 2008r2 dedicated SQL, yet SQL max resources can be set by instance and are not always shared by default. Try monitor the load on that specific SQL instance, if it is high it will have an effect on all you do in the application server.
just my 5c
the 2003 server does makes me trigger more ideas...
there are differences on 32bit and x64 setups of ePO and their supported SQL versions.
Best to have a check up on compatibility as well...