Can't Shut Down, Remedies Don't Help

My laptop refuses to shut down all the way. I get as far as a blank screen with my desktop wallpaper, but no sign of thought after that. I have to force shut down from there. I'm aware of the reset PRAM, reset SMC solution, but neither has worked after several tries. Now what?
I have a gazillion other problems related to my external USB drive, but I'm wary of linking them to this. For instance, if I eject my drive, some partitions may not eject. Trying to re-eject them results in an error -36. If I try to remount the drive, I hear a lot of whirring from the drive, but no mounting.

An update.
In addition to all the things that have been going wrong, something else has been wonky since Day 1: the Apple logo never showed up upon boot. Just a gray screen until the login box is loaded, which is nerve-wracking not knowing how happy one's computer is.
Exasperated, I went for the emergency plan. I grabbed my lappy's installation disc (not the generic Leopard disc from the box) and reinstalled OS X.
Bam! Every single problem listed above is gone. Drives eject politely and don't linger anywhere. And yes, I get my booting Apple logo back.
So there you go: when in doubt, reinstall the system.

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