I have the latest Camera Raw plugin (184.108.40.206). When I open an NEF file from a D800, the resulting image is 4912x7360 pixels, whether I apply distortion correction or not.
If I load the NEF file, do not apply distortion correction in Camera Raw, but then apply it via the Lens Correction Filter, the image must be rescaled to approximately 4840x7252 (some 98.53%) so that it matches the results of the Camera Raw plugin (minus the missing pixels around all four sides, of course).
Anyone else notice this (particularly in newer versions of Photoshop)? Is there a way to prevent this cropping? The amount of distortion on the lens (35mm) is minimal and, regardless of that, I would have expected Camera Raw and the Lens Correction filter to output identical images after distortion correction, since the lens profile is the same.
To see if that can be replicated, we'd need to now the exact version of CS6 you're running (e.g. on Mac you should be on Photoshop CS6 13.0.6) and the exact version of your OS.
Photoshop CS6 extended 13.0.1 x64 on Windows 7 Professional x64 SP1