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Repairing permissions won't fix it any more than homeopathic remedies will fix a cold.

No question it's overhyped and way too many people with systems working just fine obsessively do it way too often. But there are cases where it actually does fix things. There's certainly no harm in trying it out when a mac is generally acting wonky.
 
As Detrius, has pointed out, and I over looked... It was a hardware failure.

It was my first thought it was the update since everything started going wrong right after the install, however as it turns out one of my 4 internal drives has failed. This drive happened to be my test drive, with the beta installs of Lion on it.

Filed an RMA with WD, and should have another 2TB drive soon.
 
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