Server 2008 services disabled on reboot

As Nixphoe alluded to in his comment, your situation sounds very similar to problems people have after installing an Exchange security rollup or cumulative update. My guess is that the update installer stops the Exchange services and sets their startup mode to "disabled" while it copies new versions of the Exchange files.

Why disable the services? It probably doesn't want someone to inadvertently starting one of these services while the installer was running and the files were in an inconsistant state.

The real issue is that the installer didn't change the startup mode back to the original values. This might be a bug, or the installer may have been interrupted somehow and didn't get to perform its cleanup.

MS TechNet Forum post discussing this (credit to Nixphoe)... http://social.technet.microsoft.com/Forums/en-US/exchangesvrdeploy/thread/6ecf8e9a-9e27-4f2e-9e28-a59639029df1/

That post also has a set of sc.exe commands that will fix the service startup modes. Keep in mind that for most Exchange environments, the correct startup mode would probably be "automatic", but in failover/MSCS clusters, the correct mode may actually be "manual" so the cluster manager can control startup. It's always a good idea to check before you install an update.