This is really a simple issue. Either:
1. D/C Microsoft Security Essentials. I don't know why anyone would use it when there are known issues.
2. If the computer you are using is a dedicated computer, which it should be, then don't run antivirus on it. I certainly don't run an antivirus program on my server and never would. More trouble than it's worth. Many big time SBS gurus recommend not using AV on your server.