Sometimes when I shutdown or reboot my system it brings up a bare bones GDM screen (no theme) and sits there for a few seconds before switching off.
What's worse is often I get a horrendous succession of BIOS like beeps coming from the PC speaker while it's going down. Sometimes they beep for a second or two, stop, then start beeping again. This happens a lot more often than the first problem.

Neither of these problems effect my usage of the system, they are just very annoying and I'm concerned that they may be symptomatic of something more serious.

Has anyone else encountered this? What could it be?

My system:
Linux Mint 4.0 Daryna
Intel Core2 Duo
GA-P31-DS3L m'board
Kingston DDR2 2GB PC-5300 RAM
nvidia 8600
realtek onboard sound

Nothing strikingly odd about this sort of behavior. Some OS's scroll a bunch of text in your face during shutdown showing you what it's doing, some OS designers decide you don't need to see that useless shit and just show you a plad splash then a blank screen while all the shutdown processes are going through their motions. So be it. Especially if it operates as you expect it to when it is up and running.
This is more than likely to be a difference in the way your particular Linux distribution interacts with the mother board software (bios) during the shutdown process. Which of course, is probably different than what happens when Windows shuts down on the same hardware...stands to reason since Linux is not a Microsoft product and is bound to be different.

Anyways
Bioses do have error codes either flashed through a light on the box or by using beep codes. You can go to the bios manufacturer's site and get a list of bios error codes to dig deeper if you feel there's more to it than that. But usually these bios error codes only happen during P.O.S.T. not during shutdown. Beeps during shutdown are usually a result of old OS technology paired up with newer hardware.

Thanks, I suppose it's nothing to really worry about then.