I use the Nikon software on my Coolscan III, and have friends who use Nikon's software with their LS-2000 machines - all with good results, so.... it might be operator error. The 3rd party software that most of the top people use is Silverfast AI, but it'll cost you $350. This link will take you to the big version (AI) but there is also a lite version for $50 if you click around the site. They make it for lots of scanners and cameras, but you need to buy a copy for every scanner or digital camera you want to use.
http://www.silverfast.com/show/silverfast/en.html
Regards,
Andy Pearlman
Andy Pearlman Studio