OK this is definately another bug. The problem is connected with having a popup layer with a transition effect other than instant. If I change the popup layer I'm using back to instant the presentation popup menu goes away, but changing the layer back to slide effect and the presentation popup menu is back.

To reproduce the problem:

1: create new doc
2: create a new layer and in Layer Properties -> Pop-Up Settings change to slide transition effect
3: preview the page and notice the presentation popup when you hover mouse at bottom left