Applications become inactive and unusable, losing focus

So far this has happened with most apps.
Don't know what is causing it, but it may be Time Machine.
Intermittently, and more some days than others, applications become inactive and unusable. The symptom is when you try and switch to an application, it does not come to focus at the front.
For example, Mail is open, but I cannot do anything within the app. I can move the application window with the mouse, but cannot click any buttons at all.
If I go back to the finder and switch to Mail, it still says Finder in the top-left menu. It will only show the name of the last visited (working) app, and never Mail.
I can't find a way to resurrect Mail when this happens, including waiting patiently, using the Dock (both single click, and long click), using TAB and COMMAND to switch to the app, using the Force Quit menu to switch and even putting the machine to sleep. Nothing will fix it apart from Force Quitting the app, and restarting it.
This has happened with Safari, Mail, iTunes, iCal, Garageband (meaning lost work), as well as many Adobe apps, which suggests it is a problem with the system software.
Has anyone had similar issues, or even better does anyone know how to fix this?
Many thanks!

Create a new User go to System Preferences >> Accounts >> "+" (make it an admin acct) and test the apps in this new account, if they work the problem is isolated to your User and not systemwide.
If the issue is limited to your user account try starting up Safe Mode (It will take more time to startup in Safe Mode because it runs a directory check.)
If your apps functions correctly that way, go to System Preferences >> Accounts >> Login Items, and remove them. Boot normally and test. If not go to ~(yourHome)/Library/Contextual Menu Items and move whatever is there to the desktop. Then do the same with /Library/Contextual Menu Items. Lastly, try moving ~(yourHome)/Library/Fonts to your desktop and restarting.
Log out/in or restart, if that sorts it start putting items back one at a time until you find the culprit.
If the issue is systemwide then, you may be able to repair this with the The 10.6.2 Combo Update This is a fuller install, as opposed to an incremental "delta" update so it should overwrite any files that are damaged or missing. It does not matter if you have applied it before.
Remember to Verify Disk before update and repair permissions after update from /Applications/Utilities/Disk Utility.
-mj

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