There's a couple things I can think of.
1) Java Access Bridge is notoriously slow, especially on JRE8. If you can navigate via keystrokes, that would probably be significantly faster and more reliable.
2) If you have to use JAB, add this to your Application Modeler in the specific options field: descendtree,ignorenotshowing
I'm curious though, what do you mean by a wait on the stage? Unless this is a new feature I'm unfamiliar with, write and navigation stages don't typically come with a wait feature. I will say though, that if you're using the Sleep action in Utility - General, this has been known to halt threads. We redid it to have wait stages in .25s increments for the specified amount of time to get around this.
