Welcome to PCMechanic, thereads!
I hate to say this but uninstall NIS. It's a pain in the butt when it comes to networking and file sharing and I have a feeling it may be a part of your problem. Even if you have disabled all security functions in NIS, there will still be a part of NIS that will cause issues. Do you get any error message(s) when you try to open the two folders that you can't access? Make sure that you have the pertinent access permissions and read priveledges in the Security area of each folder.