If you start the AP Desktop from Autostart Manager, the AP Desktop window will not be displayed due to Microsoft's session 0 isolation added in Windows Server 2008.
You would have to use Remote Viewer to view any AP Desktop windows.
Starting with Windows Server 2008, Microsoft does not allow any application started as a service to display a UI.
All service applications are started in what Microsoft calls "session 0", which is a non-interactive session.
This is not a bug with AP.
You will also see at the AP Configuration Manager, when you define the Autostart and you are at Windows 2008, the 'Show AP Desktop' option is disabled.
This is because of this new session isolation.
When you need the AP Desktop, you should start AP manually after logon to Windows.