A bug that I noticed today was that the notifications come up in a new window and not the actual chat window. They do stack up nicely though as was mentioned in the changelog. I realize you had given a lot of time to sorting the notification bugs, so am not sure if this is how you meant to design it. But in practise, it becomes a bit irritating when you are talking to the person (but the window is minimized) and notifications keep stacking in another window

Edit : and I just noticed that it has been pointed out in the above post while I took my own sweet time to type