Repairing permissions takes  ages! and other apps grind to a halt.

Hi,
I tried repairing disk permissions today after noticing a bit of a general slow-down and the progress bar went about 5mm across and stopped. The animation kept going making it look like it was revolving but it didn't progress along.
I have tried quitting all apps, logging out, trying again, trying in a test account and nothing changes the fact that it takes 5 minutes approx to complete the job.
If I click on any other object whilst its determining and repairing, everything grinds to a halt: the dock freezes, action buttons go blue and stay blue, the rainbow ball spins. I've run activity monitor and it shows approx 1.6% CPU usage and the temp stays around 49 degrees C.
I recently installed Photoshop Elements but it wasn't running at the time and once permissions were sucessfully repaired it still displayed all the symptoms described above.
Anyone have a clue what's happening?
Any light shed gratefully received.

Here goes,
Ran permissions repair from DVD and it did the same thing so I clicked stop repair, the button went blue and nothing else happened for 10 minutes. I forced a shutdown and started again.
This time I went straight for repair disk and it said...
Verify and repair disk "Macintosh HD"
Checking HFS Plus Volume
Checking events overflow file
Checking catalogue file
(Red Text)-> Invalid node structure
Volume check failed
Error: the underlying task reported failure on exit
(Black txt)-> HFS Volume checked
(Red text)-> 1 Volume could not be repaired because of an error.
So, I have backed up this HD but will my clone be duff as well now or is this a physical corruption to the actual structure of the disk? I guess I can check using DUtility on my external HD.
I guess I'd better call apple eh!
Thanks, Ben.
PS - any other suggestions??

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