I just remembered that when I first started playing Skyrim on the release date, (11.11.11) and I ran into this HUGE bug, when I say HUGE I mean HUGE. It was my first time right. So I joined the Stormcloaks about a quarter into the main story. I joined them and Ulfric doesn't talk to me untill I do this quest for his right hand man. So I'm like what ever. I'll just do the main story. So I get to the peace meeting. I got General Tullius to agree. Then when I talked to Ulfric he's like "I thought you were doing something for that guy" So I'm like K? I'll do the quest then. So I talk to him he says something like he can't believe I'm trying to do a peace tready. So I can't do his quest and Ulfric won't talk to me untill I got the quest done. It was impossible to do. Bethesda please fix this if you haven't already.

IIRC, patch 1.4 fixed all weird problems with MQ and Civil War.