Verify that you have removed all other realtime antimalware products (Norton, McAfee, TM, etc). Use the removal tools here:
http://social.answers.microsoft.com/Forums/en-US/msestart/thread/407bf6da-c05d-4546-8788-0aa4c25a1f91
If you just updated Adobe Flash, you may have inadvertently installed McAfee Security Scanner.
Verify that it is not present.
Verify that Windows Defender is uninstalled (if XP), or Disabled (if Vista/W7).
Verify that you are up-to-date with patches and service packs.
Verify that your PC clock is correctly set.
Verify that you are using build 1961 of MSE (as of April 2010).
Verify that the Windows Firewall is on, and set to defaults.
In IE, reset all security zones to default level.
Then, restart your PC.
If the problem persists, submit a support case to Microsoft:
https://support.microsoftsecurityessentials.com/?scrx=1
windows 7 8 gigs ram 750gb harddrive, MSE, windows firewall, malwarebytes(on demand scanner)
