"User Configuration" - > "Administrative Templates" - > "Internet Explorer->"Prevent performance of First Run Customize settings".
Open that option and change the settings to "Enabled" -> "Go Directly to your homepage".
Group Policy Editor might not have any effect on the computers that has disabled it. You can use this registry hack to disable the runonce annoyance.
Start regedit.exe from Start --> Run and find the key:
Change the "RunOnceHasShown" on the right to: 1