I realize this is not a windower problem (as I have figured out through troubleshooting) but I'm hoping someone might know a fix for this apparently unique issue:
So my old wired controller farted out on me, didn't have this issue using that controller. New one is a wireless Afterglow PS3 Controller (Bought here) and the box says it works for PC. Got it all setup through FFXiPadConfig, and when only playing ONE character it works completely fine (although it sends input with game unfocused). But when I load another FFXI it controls both at the same time. I have "Enable gamepad when game is inactive" unchecked in Padconfig, though I have also tried it with it checked. Have used 1 as (another windower clone) and 1 as windower, have used just the native client as well and it's the same issue both times. Have uninstalled and reinstalled drivers, no dice.
At a complete loss atm, really just repeating my steps over and over again at this point.
tl;dr: 1 controller is controlling two game instances at the same time, can't figure out why.