I have this problem while working on some skyboxes for Doom, when I made the SKYBOXES lump on the WAD files inside the "basev" directory, some of them show properly (DOOM Skyboxes), but the DOOM2 skyboxes doesn't show at all, here's a screenshot of it.
I think the problem is in the way the textures are loaded from the lump, because the DOOM skyboxes come first than the DOOM2 skyboxes in my SKYBOXES lump, if you want I can also attach the SKYBOXES lump I made.