darkman in project 64 go Options->Settings..->Options and then untick "Hide Advanced Settings". Then close the Settings dialog and go Options->Settings again and all the advanced should be there..
or for graphics go Options->Configure graphics plugin... and then untick the "Hide Avanced Settings" tickbox...
another reason might be that you have restricted access to the registry on your pc and pj64 cant modify the registry, in that case there isnt a lot u can do except get Administrator access.. but i doubt it, so ignore that last bit
