Okay, I've got a fairly big bug to report to you, Apollo. This was on a new game, the only other mods I am running and have ever run (this of skyrim is a day old) are Live Another Life and Cloaks of Skyrim. I'll break everything up into sections.
Started Live Another Life mod as Imperial.
No issues here.
BATTLE FOR WHITERUN
Lost it. When I returned later in Stormcloak disguise, catapult fire was continuing to rain down on the buildings, but everything as was completely normal. I also talked to the Stormcloak general upstairs and he says what Cipius says. "Get down to the front lines, the Stormcloaks are here in force". And then the game crashed. I didn't go back to talk to him again.
BATTLE FOR FALKREATH
I noticed there was no percentage tracker of enemy troops left, but didn't worry too muh about it. Lost this one too.
BATTLE FOR MARKARTH
Okay, so I was hanging around in Morthal when I got the message to report in to Legate Adventus something or other in Markarth. This was my first time in Markarth. When I reached Understone Keep, the Jarl and his housecarl and advisor were all sitting where they normally were. I found Adventus behind a locked room, opened it inconspicuously, talked to him, and he said "Get down the the front lines, the Stormcloaks are here in force" whih started Battle For Whiterun and gave me the objective to report in to Tullius.
I used the Universal Fixed and it completed Battle for Whiterun for me, and gave me Reunification of Skyrim which wasn't what I would've liked, so I reloaded and used the fixer before being assigned the Battle for Whiterun quest, so, before talking to Adventus but after being given the objective to speak with him and defend Markarth. The fixer promptly completed Battle for Whiterun anyway and gave me Reunification of Skyrim.
I can't imagine you've intended for there to be no imperial defence of Markarth, so I think this must be a bug.