Issue when computer is left on for a while and cannot force quit anything

Hi since updating last week whenever my Mac sits for a while, I come back and I cannot use commant-tab. If I switch between apps (using the dock), I can't. I have to "hide" the top app. the app below will show but the menu panel at the top will still show the "hidden" app. If I try to force quit, the window opens but there is nothing in it to select. I have to reboot.
If I leave my computer on, this happens. If I put it to sleep when I leave, I can come back and everything is normal.
I did a disk first aid, but it is still happening. has anyone know of this?
Thanks

Disconnect all peripherals from your computer. Boot from your install disc & run _*Repair Disk*_ from the utility menu. To use the Install Mac OS X disc, insert the disc, and restart your computer while holding down the C key as it starts up.
Select your language.
Once on the desktop, select Utility in the menu bar.
Select *Disk Utility.*
Select the disk or volume in the list of disks and volumes, and then click *First Aid.*
Click _*Repair Disk.*_
Restart your computer when done.
Repair permissions after you reach the desktop-http://docs.info.apple.com/article.html?artnum=25751 and restart your computer.

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Picture of General Section of Preferences
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3) For Fast User Switching you can set iChat to go Off Line or to Go "Away" (A Status Message setting).
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Issue when computer is left on for a while and cannot force quit anything

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