Dang... I thought we fixed this particular issue. We will try to replicate it.
If it helps, here is exactly what I did to make it happen.
App was running normally.
I clicked the red button to close the window.
Dialog box came up saying something like "have to use Quit from menu to really quit, app will keep running in background".
I clicked OK. (I did not click "don't warn me again)
At this point I forget. Either the app just crashed, or I click the icon in the dock and it crashed.
Next time I opened the app I got the gui bug.