I think this belongs in this part of DW forum : https://www.doomworld.com/forum/6-source-ports/
as I am unsure that most people stumbling through those threads are qualified to answer your question. (Don't take my word for it)
It may be linked to the way you complied it.
Did you get all the level in one wad file ?
Looks like you changed the sky texture of the entire iwad.
I would check the DOOM2.wad skyboxes with Slade to be sure.
If the skyboxes are okay in the .wad iwad, then it may be linked to the way Crispy Doom reads the files, and this is beyond my skills.