This is a known glitch, it happens if you have started the Civil war questline before completing "The Fallen". It begins with the quest " joining the stormcloaks" or "joining the imperial army". If you are on the stormcloaks side of the war the main quest "The Fallen" will be bugged until you complete the "Taking Whiterun" quest for the stormcloaks. After you've taken whiterun you can continue the main quest.
A similar glitch occurs with the imperial side, details can be found on the wiki, I have not gone through it myself, on the imperial side atleast.
So regardless of what side your on, you will need to go back to a save before you spoke to the Jarl about using his palace, and continue the civil war questline, until a point after the battle for whiterun, I myself completed the questline just to be safe.