We get questions about this every so often so I figured I would send you all a heads up. A Knowledge Base article is forthcoming but it happens enough that I wanted to go ahead and get this out now.
Although a maintenance mode window has expired, an object may still show to be in Maintenance Mode in the System Center Operations Manager 2007 console.
This is caused by placing the Root Management Server (RMS) into Maintenance Mode. When the RMS is in Maintenance Mode, the workflow's responsible for bringing instances out of Maintenance Mode are unloaded, therefore when Maintenance Mode windows expire the RMS will not automatically bring them out of maintenance mode.
Placing the Root Management Server, Secondary Management Servers and Gateway Servers into Maintenance Mode is not recommended or supported as it may product unpredictable results.
Do not place the Health Service and contained objects on an RMS, Secondary Management Server or Gateway Servers into Maintenance Mode.