Instructions are for SQL 2005. If you're using a different version, check KB51620 for other instructions.
1. Identify which port SQL Server is using. To do this, go to Start->All Programs->Microsoft SQL Server 2005->Configuration Tools->SQL Server Configuration Manager
2. Go to SQL Server 2005 Network Configuration->Protocols for mySQLServer->TCP/IP
3. Right-click TCP/IP and choose Properties
4. Go to the IP Addresses tab, then scroll to the bottom where it says IPAll. Make note of the value in the TCP Dynamic Ports box, as this needs to match what your ePO server is set to use.
5. Close the SQL Configuration tool
6. Login to your ePO server
7. Change the URL to https://locahost:8443/core/config in order to access the ePO 4.0 Database Configuration Page
8. Scroll down to the Database Server Port. This value should match what your SQL Server had in the TCP Dynamic Ports box. If not, change it here so it matches your SQL Server and click Save at the bottom.
9. Close your browser
10. Now you have to restart your ePO services. To do this, right-click on My Computer and select Manage
11. Go to Services and Applications->Services
12. Stop the following services in this order: McAfee ePolicy Orchestrator 4.0.0 Server, McAfee ePolicy Orchestrator 4.0.0 Event Parser, McAfee ePolicy Orchestrator 4.0.0 Application Server
13. Start the services in the reverse order, so: McAfee ePolicy Orchestrator 4.0.0 Application Server, McAfee ePolicy Orchestrator 4.0.0 Event Parser, McAfee ePolicy Orchestrator 4.0.0 Server
14. Close the Services window
The KB article notes that doing this may lead to the Event Parser and Tomcat services to have high CPU utilization for a while until it catches up with processing, but then it will go back to normal. This is ok and you should let them finish.
After doing this you should be able to update your Master Repository, run a Pull Now, and also manually check-in packages.