Dock & Menu-bar stop responding to mouse move

Hello!
I've been having a strange problem for quite some time now. After some time of working on my mac the dock and all the menus (including the menu bar on the top of the screen) stop responding to mouse move. At the same moment also my "hot-corners" stop working. For example when I move my mouse over the dock the magnification does not happen and when I run my mouse over the menus they don't highlight. When I move the mouse to a hot corner which was attached to Expose or ScreenSaver start nothing happens there either. Whole system acts really unpredictable.
I tried killing Finder, changing resolution when this happened,... Nothing helps but a reboot, but rebooting machine so frequently is driving me a bit nuts.
Please, help!
Other details: OSX 10.5.6 (this has been happening from the start - through all versions), MacbookPro
Thanks in advance.
Y.

Ran Disk Utility off the DVD and repaired permissions and repaired the disk. Problems were found in both although, they appeared minimal. Despite that, the same issues where present when I woke it up from Sleep mode in the morning.
Whenever I hovered my mouse over the menu bar, the cursor would turn into the spinning beachball. The dock didn't freeze as it had done every time before, but if I clicked on an application it would become highlighted and stay that way without it actually opening. The opening animation never took place either.
Until some fix comes out, my next step will be checking to see what software I last updated before the problem started a few days ago and seeing if I can roll back.

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