Kyle hit it on the head, based on the information I'm reading and some other notes. The behavior you are seeing is only from premature termination of the mail process, either manual or by the server reboot, or a crash of SmarterMail. That said, there are no indications of a SmarterMail crash based on what Kyle has evaluated.
I'm not sure why you are rebooting your machine so frequently but if its for SmarterMail, you shouldn't do it.
SmarterMail shutdown time isn't based on us but what is happening with the operating system as a whole. Things like disk i/o, network i/o, terminating server connections, and much more occur when a shutdown is requested. SmarterMail, in most cases, is waiting for timeouts and or actions with other processes and we can't shut down until we get OK's from potentially thousands of different variables.
Anyway, keep your server and SmarterMail running for as long as you can because that is when we run the best. We can't possibly write everything to disk about the current conditions, and that's where memory and things we track overtime are very important for efficiency.