I joined the Stormcloaks and finished the Battle for Whiterun, and the Jarl surrendered. When I went back to report to the Stormcloaks, I couldn't hand in the quest. So I returned to Whiterun, only to find the Jarl sitting back on his throne in Dragonsreach like nothing happened—except the guards are now Stormcloaks. WTF?

I just wanted to make myself clear.