Windower Keeps Resetting Gamepad Settings [Resolved]

Trying to dual box on the same PC but because every time I open Windower it seems to reset my gamepad settings and turns "Enable gamepad when game is inactive" back on. Kinda makes it impossible to run two characters at the same time like this. So far I've tried setting both windower and ffxi config to run as admin and also running vanilla with this setting set before going back to Windower but it still reverts it back.

[Resolved]
So..apparently there is a settings window IN the windower launcher to turn this on or off, default is on.