If you are using the Coolscan 9000 with a Mac, the way I've always handled the issue you describe is by trashing the Nikon scan preferences and rebooting Nikonscan. Years ago a Nikon tech told me about this. When the scanners are used for a period of time, the scan preferences can get corrupted. So you need to trash them, and if it's really bad, repair disk permissions, restart the computer, and relaunch Nikon Scan. Then I usually Calibrate the scanner again. This has always fixed issues like the one you describe.
To do this on a Mac, go to Users/UserName/Library/Preferences and open the folder titled Nikon. In that folder you should find a file titled Nikon Scan 4 Prefs. Put that file in the trash, empty the trash, and for safe measure, Repair Disk Permissions in the Disk Utility app. And finally, to be really safe, re-start your computer. Although I usually just delete the Nikon Scan 4 Pref file and restart Nikon Scan.
Then make sure to Calibrate the scanner after doing this and you should be good to go.
Best,
-Tim