Set the environment variable MODS_PRESET to the HTML preset file exported from the Arma 3 Launcher. After it 'updates' my personal files, and I try to join my server through the A3Launcher I get the bad key error.
This folder also needs to be lowercase in order for the server to load the required PBO files inside. Yeah, I just let the A3Launcher 'update' and slowdownload the epoch mod files again because (according to it) my files didnt match the server files.