Mine was a total dog too. Sometimes it seemed to just go to sleep after making an edit, and the tray icon would indicate "not responding". Eventually it would wake up, but processing files this way was painful to say the least.
Out of desperation, I uninstalled Capture NX. I also uninstalled Nikon Capture 4.whatever that was still on my system. I then (after rebooting) reinstalled Capture NX 1.2, and then the upgrade to 1.3. It's now much faster, and the sleeping syndrome is no more.
Don't have any idea if that'll work for anyone else, but for me uninstalling and reinstalling did the trick.
