Odd/Limited Mouse Behavior

I have an intermittent problem with my mouse behavior in 10.6. Actually, I'm pretty sure I had the same problem in 10.5, it's just a fiendishly intermittent problem that has an as yet undetermined cause & solution. All I know is that it occasionally occurs and eventually resolves itself.
What happens is that I can still click things, scroll, right click to open a more extensive menu, etc., but certain ancillary (yet surprisingly critical) functionality stops working for a time.
For example, hovering my mouse over a link in Safari does not turn the pointer into a "hand with an extended index finger" or does not cause embedded pop up messages to appear (on sites I'm familiar with, no less, so I know they have them). On my Safari browser tabs, the 'x' to close individual tabs does not appear unless I first click on a tab once, and it closes when I click it a second time.
In menus - anywhere, not just in Safari - clicking on File or Edit or View opens the window, but selections do not highlight and track my mouse movements the way they normally do. This makes submenus impossible to use without clicking and holding once I reach the submenu I want to open, and releasing the click when I reach the option I want to select.
The Dock, which I have set to Show/Hide based on my mouse movements, will not pop up when I move my mouse all the way to the bottom of the screen. If I click my mouse once while the pointer is essentially invisible (being at the extreme bottom of the screen), the Dock will sometimes appear, but not always. When it does appear, the icons in the dock do not enlarge/magnify based on my lateral mouse movements the way they normally do.
In iTunes, when I'm watching a TV show or movie in full screen mode, the controller does not appear when I move my mouse the way it normally does.
And so on.
I have never found a working remedy for this affliction, I usually just have to ride it out, i.e., I deal with the limited functionality until something decides to work right again. I have reset my mouse (it's a wireless Logitech mouse with five buttons, including the scroll wheel, but I had a wired mouse way back in Leopard), I have restarted my Mac, reset Safari, reset my System Preferences, repaired Disk Permissions, I have even junked the entire Preferences folder and restarted. I have also switched to different mice, but they have the same problem while the problem is occurring.
I don't believe this is a settings issue, I think it has something to do with Java or something, which occasionally goes on a holiday.
If anyone has any ideas, I'd love to hear them. I've been enduring the issue the last day and a half and this is the longest it's ever lasted without correcting itself.

Check for any dust in the LED hole. Try using a plain surface, like a solid colored mouse pad, if the surface is on the shiny side. If that does not work...
Try starting up from Mac OS X installation disc. If the mouse is also erratic when booted from another system, you can rule out the 10.5.3 update as the cause.
If it works normally when you are booted from the installation disc, there is probably some issue with your current installation.

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