I think its the default behaviour until all mail is delivered/archived in the right places and everything is syncronized.

Wait until it dissappears from task manager and youre good to go on an upgrade.

This isn't a normal behaviour. When the process is still running, the Windows service isn't stopped. Yes, the MailService process needs some time to stop as you described but then the Windows service shouldn't be shown as stopped! I don't know any other services with this behaviour. A Microsoft SQL or Exchange Server process also tooks some time to stop when stopping the service but the service doesn't show that it is stopped when the process isn't stopped. And in the past the SmarterMail service didn't show this behaviour.

As Brian pointed out this is expected behavior as SmarterMail gracefully disconnects any clients actively using their accounts. We have made improvements to service lifecycle management in our upcoming release (currently in beta) which should handle this much better than the current results however and you should see a quicker shutdown when that new version is available.

Stefan, that is not true about SQL Server (and also a few other services that I have worked with). When we shutdown one of our shared SQL Server instances, the "stopping..." activity form shows for about 20 seconds or so, then goes away, indicates it is "stopped", but the process is still running. It takes about 10m for the main SQL server process to close up resources, drop connections, write data out of RAM, syncronize etc.