Anyone experiencing this should download the patch on larianvault.com under your games.
Savegames affected by the "waiting for commander" issue will not work anymore.
Savegames that have council issues will be backwards compatible with the new patch, that will normally be online later today.
Greeeat. So my saves are pooched now. I am very disappointed in Larian right now to let gamebreaking issues out the door like that.
Live and learn I guess. Just don't count on my future support.