Mods select but can't be played

I have mods that are in the Mod folder, show up to be selected in the game (and are listed as selected at the setup screen), but don't show up as options in the scenario list. Old mods I made (including some I've deleted) show up as possible scenarios but not the new selected ones. Can the scenario list get full? How do I remove old mods from that to make room? Is there some other explanation?