I use Capture NX too, Version 1.2, and I've never had a problem like that.
I basically use it for converting RAW to TIFF (on the assumption that a Nikon program will do this best for Nikon images), and sometimes do a little bit of processing in it. But i do most of my post-processing in Photoshop.
Didn't know there was a version 1.3 out. I'm off to download it now. Thanks for the info.