Well I've set the path to my Noggit WoW client directory so it loads the files from there.
It's pretty odd I think that Noggit crashes when trying to load the custom map when having other WoW test client and WoW server running. The log file seems to be "clear" (meaning that there are no errors).
Oh, and by the way, noggit crashes also when trying to open any map, not only when loading custom maps.
And after closing the WoW server and test client I can open all other maps than my custom maps.
My Noggit WoW directory is clear (no custom patches there).