Yes, I have lots of mods installed; they're all BOSS-sorted with a few tweaks recommended by authors, with a Bashed Patch, and any appropriate compatibility patches applied. None of them directly affect the Dawnguard quest, any of the Dawnguard NPCs, or any of the Dawnguard-specific locations except for SkyRe(which hits pretty much everything in the game at some level, and I found no mention of any other SkyRe users having this issue) and Freedom of Speech(which just moves one Word Wall).
My game is patched up, and I have all the Unofficial Patches other than Hearthfire(since I'm not using that DLC on this character).
I saw the cutscene, it played out in-full, and the quest-complete blurb came up on the screen with its wee drumroll sound. I confirmed the quest was complete using the console.
I cannot speak to everyone, because as I said, the problem is that Serana is not present. I searched the entire castle, and the entire area outside the castle. i did so again after waiting for ten ingame days. Serana never appears, Isran never has an argument with her, he just stands there on the balcony or, if I wait outside for more than 24 hours, in his room.
I have done everything I can think of, I even went on a fast travel tour around the map and slept in several inns. Nothing seems to work, Serana just never appears.
Attempting to force the quest to start via the console doesn't work either - it generates no errors, but after putting in "setstage DLC1VQ03Hunter "(and I tried it with stages 0, 1, 5, and 7), using showquesttargets doesn't have either A New Order or Prophet listed, and no Dawnguard quests appear in the quest log.