Mouse click bugged

Hello.
I've spent a few days now troubleshooting this problem but I guess I'll have to refer it to the boards, I'm utterly stumped.
My mouse clicking has started cutting out intermittently.
The Symptoms are these:
When in an application such as safari, my left or right click (using a mighty mouse) will be ignored for long periods of time, or only be registered after 50 or so clicks have been made. The mouse still tracks fine and I can often click UI elements or links within the page but can't click the main menu or some of the other UI elements. I also can't click into another application to change the frontmost application.
However, at all times I'm able to click on the finder in the background and drag around folders and whatnot.
First of all I presumed it was simply a case of Safari, Text Edit, iChat etc not being the frontmost application. However the menus at the top always showed the correct application as being active and never displayed the UI elements as faded as would be the case with an application which is not at the front.
Sometimes switching too and from the application window will restore click sensitivity, relaunching the finder also works. However the clicking bug will return only a few seconds later.
Things it's not:
1) It's not a universal access problem. Made sure this wasn't active
2) It's not a fault with the Mighty Mouse. I checked it on other computers, works fine.
3) The mouse hasn't been incorrectly configured in System Preferences.
So basically the situation I'm in now is that any application will spontaneously lose mouse clicks as if some phantom application was running in the foreground absorbing them. The only exception to this rule is the Finder which works at all times (but from which I can't select other windows to bring other applications to the foreground) and who's quitting will reset the bug temporarily.
No other applications are running, my knowledge of the process IDs for various system level processes is poor but I'd be able to notice anything than totally out of place applications running in Activity Monitor.
Some UI elements are unaffected by the bug, such as finder panes and scrollbars, others are such as title bars, traffic lights and control buttons.
I'm at my wits end, in over 15 years of using Macs this is by far the most annoying bug I've ever come across (thankfully I've not had many others to speak of) and one which I'm completely baffled by.
Oh and the latest security update is installed.
(right now in fact, I just went to go click on the apple menu from here in Safari and it won't register my clicks, none of them - I had to tab out to the finder to click the apple menu)
Dual 2ghz G5   Mac OS X (10.4.6)   2.5 GB ram

Yup, thanks.
I had to use the preferences to work out what the problem was - I had a hunch because safari was opening any link I clicked in a new tab so I set the middle button to open spotlight. Sure enough, every click I performed with the mouse triggered spotlight.
All I did was deactivate the middle button action and I could get a single left-click working fine. However, since the Mighty Mouse interprets Right Mouse + Scroll Ball as Middle Click, I'm left without a right click.
Quicksilver (2002) 933mhz   Mac OS X (10.4)  

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