Thank you for your reply, I'm glad to read that you found the white rectangular culprit :-)
Regarding the "not responding" dialog: I'm afraid starting the game in fullscreen doesn't help, I already start it in fullscreen. Switching to windowed mode just puts the game into a window, but the dialog still appears at the beginning. At the positive side, I never have to switch out of the game, the mouse works perfectly fine.
I just noticed that the game always makes full use of one of my 8 cores after the Unity logo disappeared and before the menu slides in. It's just for 1 or 2 seconds, but that's around the time where the dialog appears.
If you need any further information, just let me know.