This seems so obvious a problem that I’m surprised everyone isn’t complaining. Maybe that means it is something specific to my PC’s configuration.
Having installed MS-Antispyware, whenever I launch a batch file using a shortcut a warning window of some sort scuds up the right hand side of my screen too quickly to read – let alone try clicking on its buttons. Specifically this is a problem when launching Cygwin (the "free" POSIX shell environment) from "quick start". The only way I’ve been able to launch Cygwin has been to disable MS-Antispyware. I do not believe Cygwin to be a spyware threat – but even if it were, a warp-speed-warning that can’t be read isn’t a particularly helpful countermeasure.
The window is unreadable because you have the start bar docked on the side of the screen. This is a known issue which we are working to fix in a future release. As a workaround, dock the start bar at the bottom of the screen and allow the application change.