I use a Nikon Supercoolscan 5000 ED, which I bought last year. I have been scanning 25-year-old slides of non-Kodak film (probably Agfa, which have faded and turned pink. The Digitial ROC (recovery of color)software bundled with the scanner does a good job of restoring lifelike color--BUT after a few scans (the number varies) the scanned color and contrast become clearly distorted. The only way to cure this that I have found is to quit the Nikon Scan 4 software and relaunch it. Having to do this repeatedly is both tedious and troubling. Is anyone else aware of this glitch and know the source of the problem--and maybe a fix?
Instead of using the scanner software to correct color, have you tried just scanning and using Photoshop to do the color correction? The correction you're speaking of sounds like Auto Color in Photoshop but you should try it to be sure.