I always put a note on my threads.
Manual Dimension would work too. I have had this same problem frequently and I do like what Steve does, put a note on the thread or just manual dimension works too.
You can also try to re-do the drawing file(start a brand new drawing from scratch) and hope for the best. sometimes it works, sometimes it doesn't.
I always use the hole callout so you get the drill and tap information for the holes. I can't say I ever put a thread note on like that, although I did just try it on a 1/4-20 on a section view and mine aligned like it should, so this is not a problem all the time I would guess.