Please excuse me for making silly suggestions, as I have no direct experience of the matter, but I wonder, if anybody has had the chance to see whether Dawnguard would show any signs of this issue, and whether there might be anything different about how new quests in it are set up?
If Dawnguard does not suffer from this issue, but user-created ESM-mods do, there must be a difference somewhere, and hopefully that difference might be observable, if it is in the ESM rather than hidden inside the game engine itself.
Also, I tried reading this thread very carefully, but in the end I did not get a perfectly clear picture of whether the following is strictly true, which I would think is very essential for understanding the nature of the issue:
I was especially confused by the following:unless there is something I missed that would reconcile these observations.
See? Obviously Dawnguard does suffer from that new form of dialogue bug! I'd like to add, that I already noticed the "SayOnce" problem with some thieves guild dialogues (not only Delvin, but Vex and some fences, too) BEFORE patch 1.7 - with version 1.6.89.0.
Oh snap.
So then hopefully this shoots up on Beth's priority list of things to fix. :/
There are at least two places in the quest line in Dawnguard where it looks like the dialogue quest might be the issue.
http://www.gamesas.com/topic/1402261-volkahir-keep/
This one hasn't happened to me.
http://www.gamesas.com/topic/1402253-bloodstone-chalice-wont-advance/
I was the first one to report this, but there is one other person who has reported the same thing. The Vampires in that fort do not recognize that my character is now a vampire so no dialogue options are available.