Why do I still get alerts after putting a computer in maintenance mode?

When a computer is put into maintenance mode, the database and the management server are updated immediately.  At that point, any server side responses including notification rules will not run.  The agent will be polling the MS on its polling interval (default = 5 min.) as usual looking for configuration updates.  Until the agent makes a configuration update, it will be unaware that it should be in maintenance.  It will continue to generate alerts and run responses until it gets a configuration update.  So – on average, by default an agent will continue to generate alerts for 2.5 minutes after being put into maintenance mode.  Similarly, on the flip side when an agent is taken out of maintenance mode, on average it will be 2.5 minutes before it starts to generate alerts and run responses again.