Sorry for late reply.
I'm using DOOM2 as an IWAD, doom_complete.pk3 generated with the latest version of WadSmoosh (incl. the Master Levels).
I think the problem was caused by me using the DoomLauncher to run the mod, and probably something went wrong with loading order. I've just ran the mod by making a shortcut to gzdoom with appropiate -file parameters, and the maps load as they should.
Super sorry for confusion!