I've edited the resource.cfg, even tried deleting it, but nothing is working. If the Mod is working properly, click the icon in the top right portion of the Civ 5 game screen or press Control + I. You can now select Single Player and set up the game as you normally would. I don't have any subfolders, and all the mods are. Load Civilization 5 and select ‘Mods’ and ensure that Ingame Editor is checked, then select next. I had this problem when I first started playing, and was able to fix it, but I don't remember how since that was a few months ago. I've even tried running my first file, and even swapping the new mods with all the old ones, and they won't even pop up then.
I have it checked to allow mods, I've tried restarting my computer, restarting my file, checking for bad mods, deleting them entirely. Though I've tried everything, none of my mods are showing up in the game, I won't even get the popup in the beginning. After that, I installed some new mods and kept some of the older ones since I'm pretty sure they weren't the bad ones. (Which meant backing up my folder before deleting it entirely and then starting the game, which restarted my game entirely). Everything was fine, so I went to create a Sim, only to be unable to pick traits or aspirations, which I looked up and found out it was a faulty mod or something like that, and after trying everything I just decided to restart my file. So I recently installed the Sims 4 again, and had to re-enable mods after the newest update.