It's a bug linked to destroying the codex. If you take the other darkside option (give it to Darth Jadus) you can proceed fine.
I ended up doing that even though it isn't the ending I wanted, cause who knows when this is going to get fixed.
Ahh... you could be onto something... I chose only light side options so my option was giving the Black Codex to Minister and being free from the reigns of the Sith. I encountered no problem with the options I was given.