GZDoom doesn't load certain wad files

First time setting up GZDoom. Works fine with the vanilla doom.wad, doom2.wad and heretic and hexen.wad files. 
I also bought Doom and others again on Steam, to have the extra levels, never had those before. GZDoom autodetects those Steam installs and loads them fine.
However, when I copy those WAD files from the Steam install directories towards my GZDoom folder, GZDoom doesn't load them, doesn't show them in the launcher, and when dropping them on the gzdoom.exe, nothing happens at all. I don't want to use the autodetected Steam stuff, I just want the wad files to work.
When I load the same wad files with RetroDoom, they do work.
What am I doing wrong?

Seems that when I have the vanilla doom.wad and the ultimatedoom.wad files in the same folder, GZDoom only sees one of them. Even when dropping the ultimatedoom.wad file on the exe it doesn't work.