OK so after a lot of hassle (over a year trying on and off trying to get windower to work, i finally managed to get it working. It turns out there is a file/addon/app called Direct Play. before installing this it crashed on the usual PLAY button 1000% of the time. However as i was starting FFXI up again with Windower, it asked me to install Direct Play. Upon doing this, the game with windower running all my plugins barring Spellcast which is no longer there, booted all perfect!.
I hope this helps someone and possibly could lead to something for the devs to follow up on
Thanks
CP