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I couldn't replicate your workflow as once the raw file is opened you cannot do...

...your step #3.

In order to save the file as a PSD I first need to finish editing with Camera Raw but after doing so I still couldn't replicate the problem.

You didn't stipulate whether you are using the 'Extended' version of CS6 or not but as far as I'm aware any raw file opened via PS should open in Camera Raw first...regardless.

You make no reference to Camera Raw so I can only assume that raw files  are being opened directly in PS and not Camera Raw as normal.

If your installation of Camera Raw has become corrupt and PS is unable to access it then this may be part of the problem, but Its difficult to say for sure.

Without being able to replicate your workflow, let alone the problem, its difficult to suggest anything specific to try.

Resetting the prefs files as [USER=69670]IamSam[/USER] has already suggested is therefore the most logical thing to try first.

Regards.

MrToM.