Are you clicking on the PI App Icon in the dock? If so, try clicking on the PI Window Icon in the dock, you know the one off to the right, after the little dock divider, where all the running app open windows are shown. (Not sure of the exact terminology here). I find that after minimizing PI to the dock, I have to click on the window icon to restore it. This may be because I'm running dual monitors and have placed the Console and History Explorer windows on the second monitor.
I hope this helps,
Sean