Its weird one but I fixed it ,it still puzzles me though why it did occur in first place.
So i created a bishopric in Geneve. However the county appeared as part of my demense - though - the game didnt treated it as such and told me that i have 2 demense provinces instead of 3. But i could still click around it and build new improvements. Now the bishop.. he was in my court! With that round county mark around him u know
and he even demanded to become my diocese bishop!
i mean how bold is that 
Anyway i was wondering what to do, and after some years (mind u that i could save the game, then reload and the situation was the same) i decied to give him another title. So i made him hold 2 count titles and it was all fixed.
Suddenly his primary county got the Controller flag of my nation on it, and the after some time it disappeared.
Fin

So i created a bishopric in Geneve. However the county appeared as part of my demense - though - the game didnt treated it as such and told me that i have 2 demense provinces instead of 3. But i could still click around it and build new improvements. Now the bishop.. he was in my court! With that round county mark around him u know
Anyway i was wondering what to do, and after some years (mind u that i could save the game, then reload and the situation was the same) i decied to give him another title. So i made him hold 2 count titles and it was all fixed.
Suddenly his primary county got the Controller flag of my nation on it, and the after some time it disappeared.
Fin