Dock looks screwy, clock is missing and LMB not working on desktop

This seems to touch on several parts of the os at once:
I maintain two iMacs in a retail environment - the accounts are managed and the users can only access some basic functions of the OS plus our POS software. They can't install apps or adjust settings so there's little they can do theoretically. All software is either in the OS or is made for 10.6 (MS Office on one machine, Salon Transcripts on both)
I first had this problem on one iMac that had 10.5 (the rest were on 10.4) and out of frustration, I upgraded both machines to 10.6 and now the problem happens on both.
1. Left clicks don't work in dock (3 button mouse. hover works, right mouse button works) or on desktop icons. Can't launch new apps but can cmd tab to active apps. Once in an app, LMB clicks works fine.
2. An open app might leave a copy of itself on the desktop (like a buffer not refreshing) except that I can launch the app over that image and the image will remain. It's very confusing to the users who don't know how to tell the difference.
3. The dock looses it's background graphic. The dock's mirror effect ends up mirroring everything in the lower part of the screen - apps, desktop, dock icons, etc. so the bottom inch of the screen is just a mirror of the inch of screen just above it.
4. The top bar clock and all icons on the right half of the bar are missing.
A reboot fixes all of the above for a short while and the problems return. This is really frustrating and debilitating during retail hours. Suggestions or fixes are welcome.
hardware: both are iMac 17" core 2 duo MA590LL/A, 1Gb ram, 160GB drives that are mostly unused.

Unlike SideStepSociety, I've never +wiped an HD and reinstalled from scratch+, finding it to be total waste of time. I've beta-tested every OS upgrade from Panther through Snow Leopard and always just upgrade them, ensuring that I have tested bootable backups/clones to revert back to. The only time I install the OS onto an empty volume is to test that the setup assistant does its magic by migrating from the previously good OS. Once I ensure that the procedure works, I wipe the HD, put a clone onto it, and upgrade it.
As for your query, if the original is mucked up, so will be the backup/clone. I use Carbon Copy Cloner instead of SuperDuper!, but both are viable.

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