Yes, the MainMenu.xml is the legacy menu format. It now uses "menu.xml" in the settings. It seems that the installation has gone wrong at some point and that "menu.xml" doesn't exist, hence it's searching for the legacy file. Or that menu.xml template has been deleted??
I don't think it's linked to the skins, have you tried it on a fresh install of DNN?
I don't think it's linked to the skins, have you tried it on a fresh install of DNN?