Mac Pro All Keyboards/Mice Unresponsive

I was wondering if someone might be able to help with an unusual problem I'm having with my early 2009 Nehalem Mac Pro (2.26hz). I have been having a recurring problem where when I turn the computer on and it boots up, my cursor (apple wireless might mouse) can be moved on the finder, but nothing on the finder will respond to mouse clicks. Similarly, my small aluminium wireless keyboard will not respond in any way.
Thinking this is some kind of wireless issue, I will usually replace the batteries in both mouse and keyboard, try resetting the pram in the mac (and pressing and holding the power button with the power disconnected etc). Sometimes this will work and I can get up and running again with wireless services, sometimes not. This morning, it remained unresponsive after several attempts - I plugged in a wired mac keyboard and mouse, and the computer would not even respond to these, even though it would boot up into the finder. After another half dozen attempts at hard shut downs and letting the computer go through its lengthy re-start process, the wired keyboard and mouse were eventually recognized, at which point I could unplug them and turn on my wireless mouse and keyboard, and I'm up and running again.
Can anyone point me to where the issue could lie? Where a solution could be pursued? Any particular preferences etc that could be corrupted? It's a frustrating problem that is making me hesitant to shut the computer down at any stage in the event of not being able to operate it with either wireless or wired keyboards/mice.
Thanks - Steve
Message was edited by: oceanicrecords

Thanks Dale - I've only tried permission repair, however I will run diskwarrior over the system drive and give that a go now you mention it....
Steve

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