It seems gzdoom has a fuzzy finder for IWADs. This means that if the iwad file name isn't exact it will load another IWAD.

For an example if you have DOOM.WAD and DOOM2.WAD and load with gzdoom -iwad doom.wad. Gzdoom will open the DOOM2.WAD.

Looking at games.json . twad isn't preserving casing and it seems to exacerbate gzdoom somewhat. Editing the iwad filename to be correct again in the json returns normal iwad loading behavior for gzdoom.