I've just started Dawnguard and found Serana. Her dialogue options don't seem to recognize that the Civil War questline is over. I'm not sure if this is purposeful or not, but this isn't the first time I've had a Bethesda game's dialogue script ignore a previous questline and totally break the game for me, so I decided to not proceed until I'd gotten some sort of answer.

I've tested it multiple times, both with my mods and with all mods uninstalled. I get the same behavior all of the time.

Wow, nothing at all? Not even someone saying 'yeah this happened to me too'?

Its possible the mods made changes to the game data and they have been stored in the gamesave. Frankly you should not even be using mods with DG until they (the mods) have been updated to make them compatible. Otherwise issues like this and many others will crop up.

Yeah, I'll probably restart from an earlier save once all the mods are updated. For now I've just disabled all mods, verified my game data, and started a new game.