Notably, there isn't a single AddSearchPath log line referencing the Mods directory anywhere in the game log — only the base gamedata (c:\programdata\faforever\gamedata*) and Steam install directory (f:\steamlibrary...) get mounted. It seems like the game's file system isn't mounting your mod folder. Check "C:\ProgramData\FAForever\fa_path.lua" to see that custom_vault_path is correctly set. ProgramData\FAForever\bin\init.lua uses that value to determine what folder to mount for your maps/mods. The only way that could be broken is if you set a different init file in the client's launch args (unlikely that you did that).