Problem is starting again, I've diagnosed it a lot and now my conclusion has changed.
The problem with the hard drive was corrupted data, and SMART had failed.
SMART was fixed and all my different software(5 different bits of software) and it's now working perfectly.
However I'm still getting the problem above only after strenous use of my video card.
If I revert to software renderers it dissappears and doesn't come back until I use my video card heavily once more.
The sound is one click with a whine(Sorry I didn't say this when I started the thread, WD site cites this as being normal). Then the game/application skips a lot and pauses like in my original post.
My video card is dying, and these are signs of it occuring. It's almost 4 years old, been overclocked a fair bit.
My friend had his Radeon 9700 Pro (Never OC'ed it once) for 3 years and it's already unusable in anything 3D accelerated.
It displays severe corruption in anything 3D.
How long does it have until my video card dies or becomes unusable or a hinderance to use?