Did you try file check before clean install? That may work.
Open POL and click Check Files:
From the drop-down box, be sure to click Final Fantasy XI and not Playonline or Tetra Master:
I've heard this works. Give it a try.
I'm far from 100% sure that this is a fix as I havnt' confirmed it myself with this yet, but I have read if helped other people with problems that popped up after the most recent version update.
Good luck!