Im running NL from an external drive that also functions as the drive that holds the my documents folder. I just set any programs that use NL (track packager, construction kit, update patcher) to the file in my external, and ive got short cut icons and dummy files that refer the program to the actual directory when it looks for nl files on my c drive.
Also, NL uses various registry settings, so you might wanna back-up your registration key and track files etc. and re-install NL to your c drive. If that dosent fix the problem, it might be your computer.