Comment 14 for bug 765084

Changing the layout, destroy the current window and creates a new one, so I guess that's why unity notices the window correctly after that. I've seen a few bug reports about unity loosing the active window, so I would say it's likely it's unity's fault.

About the resolution, yes that probably explains it. You should use a layout suited to your resolution anyway.
I guess I could add a message, when it is creating a window bigger than the screen, that propose using a smaller layout, I'll think about it.