Hey Edorhunter!
I’d read some of the comments on wowhead here for the quest: A Message Most Dire
In particular, I think Vylun’s comment may help:
Just stumbled onto the same issue; go to Tyrhold, a short flight towards the east where Alexstraza is waiting (you can see it from the top of the tower, another tower with a lightbeam shooting up from it). Complete the two quests there; killing a dragon and finding Alexstraza. After that there’s a weird double up, her dragon form flies back to Valdrakken and her human form stays outside the dungeon entrance. Her dragon form is now in Valdrakken again, able to interact.
Basically if you have the quest To Tyrhold (or maybe any of the quests in the chain?) Alexstraza will not be available until you complete them or abandon the quest. I’d complete them.
Hope that helps! 