Main window appears in the background but cannot be selected/interacted with while the setup wizard is running. Note that the main window also forgets to draw itself--it shows up as unpainted/corrupted video memory until the wizard is done, then begins painting itself as it should.
I speculate that it is not processing paint events while being interrupted by the setup tool.
What window manager/compositor are you using? The main window is meant to be hidden during setup and that has been the case during my attempts to reproduce
I speculate that it is not processing paint events while being interrupted by the setup tool.