I have been using the alpha versions since they came out and really have had no issue with them. With 5.2.1 Alpha 9r1 most everything was good. I noticed the end of quest issue but could live with that for a while.
With 5.2.1 Alpha r2 my quest watch operates normally with one toon (my main) but with every other toon I get nothing under the quest watch icons.
I log back onto my main toon and quest watch seems to work fine.
Update. I had already logged out and back in a few times through out the night so I log back in and went into a 5 man heroic and came out and my quest watch seems fine now. Wierd.