Have you got more than 1 WoW folder?
I've about 3-4 and i had to delete the install and gamepath in regedit, start 3.3.5a wow and then i could use noggit.
If your game and installpath are to a wow folder with another version, it won't open.
Or you check your noggit.cfg if there are the right paths
#Path = WoW
#ProjectPath = WoWData
If this doesn't work for you, wait for someone else who got an idea what that could be.