Quick question, is there something special you have to do to install mods for AB+? I just now realized that none of the mods I have installed work when I load up AB+, but if I uninstall it and just play AB it works perfectly. Am I doing something wrong?

Seems there was a patch today that makes the game load up packed files first before the loose ones. Trying to work around it now, renaming the packed folder might work but need to have all the files unpacked first instead of just the ones you want from mods. You can use the unpacker in the tools folder of the game.

https://www.reddit.com/r/themoddingofisaac/comments/5mtl0b/how_to_enable_achievements_for_resource_lua_mods/