I want to bump this. Literally almost the same problem happened to me, and I found no fix for it. Trying to manually advance quest stages doesn't work, either. For whatever reason for me, every stage except stage 1 and stage 255 (finishes the quest) actually exist in-game, and the only things I'm running are Skyrim patchted to 1.9, with all DLC, and the Unofficial Skyrim patches (also the patches for all the DLC). I got stuck with "Liberate Falkreath Hold", but finished the main quest line without starting that, and all Ulfric wants to do is tell me they've stopped the fighting... Everywhere I've looked, though, there's no sign of any glitch like that anywhere. From what I've seen through the forums on other glitches, over time the save corrupts in some weird way over time, causing it to sort of... break things. In this case, it seems to 'forget' the existence of quest stages. Trying to push through Civil War from the get-go, like Kaikasu said, seems to allow for regular progression... I've yet to test further, but I plan to try pushing my way through the main quest (avoiding side-quests), then doing a play-through with Civil War up to the Battle for Whiterun followed immediately by Season Unending (like I did in my main playthrough, minus side-quests).