New KB article: Management servers or assigned agents unexpectedly appear as unavailable in the SCOM Console in Windows Server 2003 or Windows Server 2008

Microsoft has released a KB article (KB981263) which addresses above mentioned issue. This issue might occur in SCOM SP1 and SCOM R2 as well.

Cause and resolution to be found here. It is all about an issue in the storage engine of the jet database that is hosted on Windows.

When downloading it for Windows Server 2008 you can select the Vista option since it has the same code base as Windows Server 2008.