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Which IWAD are you running the mod with? It depends on having a doom_complete.pk3 IWAD created with WadSmoosh that includes the Master Levels files.

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!

No problem! Yeah it's expecting the equivalent of this command line:

gzdoom.exe -iwad doom_complete.pk3 -file masters.pk3