it happens to me too, after they have been eliminated or in some cases, assimilated, thier influence score still shows up in the UP section of the foriegn stats window. They don't appear in the actual UP event though if they are no longer a 'sovergn entity'.

I have this too, think its a minor bug with 1.2?

You can also have a seance in the Foreign Relations window. It remembers the last faction you selected to Speak To and opens with that faction still selected. That's good programming.

What's not quite so good is that if that faction was eliminated since the last time you opened the Relations window, they remain selected even though they're no longer available for negotiations.

Last time this happened to me, I had finally ground the stupid Iconians into cosmic dust. Iso's ugly face appeared above the Speak To button next time I went to Foreign Relations, and I really wanted to click the button and ask him how eternity in the deepest pits was going... but I have enough ctd's with my older computer and didn't want to risk it. Sigh.