I've looted 21k eddies before my first meeting with Victor, and i've paid that 21k for my new Kiroshi eye implant. BUT when i got up from his chair there is the a dialogue about my 21k debt that i STILL OWE TO HIM.

That's probably just poor dialogue writing.
Do you still get the quest to repay him in the journal? Is it 'Completed' or still active?

If the quest is active or missing, best bet would be to reload a save, not pay him until after to complete the quest.

Maybe that worked, anyway after Kompaki prologue there's no more debt)

It's a known bug, the game don't expect you to be able to refund him the first time you met him, so if you do the dialogue will be bugged. But normally it fixes itself if you leave and come back later.