I don't think focus is being taken away. If it were, the message box be displayed momentarily, and I do not see it appear at all. Normally, message boxes are not dismissed when they lose focus, so Start11 must have some code watching for lost focus. Perhaps that code is being triggered accidentally. (Although, I think I'd still see the message box appear momentarily.)
I did a full clean re-install (uninstall, reboot, manually delete all remaining folders in %appdata% and program files, reboot, install). Maybe that helps?
Sorry, I tried that already. 