Halfway through the battle with Glacias in Nalias Castle he realises he had been possessed and runs off. Does he have the third head of the Flail and if he does have I lost the chance to complete it? Can anyone help?

Never heard of this happening before. Yes you have lost part of the flail. Try a reload and block the doorway.

After he turned yellow, I chased that dude from one end of the keep to the other until I finally killed him!!! He ran downstairs near the front entrance, then ran back upstairs the other way to the library, where he met his doom.