I am also currently having this issue on my Mod.
I realized that the steam workshop renames the file when it moves it to whatever the name of the mod is on the workshop. So I removed the "/" I had in my mods name, but that still has not fixed it yet.
My mods name is Paladin Class. Originally named Holy Hydrosophist, it works fine if you manually copy it over to the mods folder, but doesn't work if just subscribed.