By "the GDC will not appear at the top of the screen", do you mean the GDC application will not have Windows focus, as opposed to the other possible meaning of the window y position = 0?.
If you mean the GDC application will not have Windows focus, and hence the GDC window does not showing in front of the other windows, this is due to the default behaviour of Windows operating system. An application, In your case explorer.exe, can pass the focus to a new application, gdc.exe as in the case when you first double clicked. A running application cannot steal the Windows focus from the current application, so when you start the second Genero app, you are effectively wanting the existing gdc.exe application to steal the focus from the explorer.exe application.
This Windows behaviour was introduced many Windows versions ago, either XP or Vista, and the best way to explain it, is if you recall early mail apps would popup a dialog saying 'You have mail, would you like to read it Yes/No' but you would be typing away in another app and if you weren't looking at the screen, then you might answer the dialog without realising it. So this Windows behaviour was introduced so that an application e.g. Outlook.exe would not be able to steal the focus away from the current application e.g. Word.exe, but would instead flash in the taskbar. If you look at your video carefully, you will see the GDC icon in the taskbar flashing when you launched the second Genero program.
When you use gdc -n, then it is launching another instance of gdc.exe so Windows focus can be passed to it, it is not a case of the existing gdc.exe trying to steal the focus. You also may see this if you double-click on two .txt files, two instances of notepad.exe are started.
You can change this behaviour by changing the value of some registry settings. Google "foreground lock timeout" and "foreground flash count" for more of an explanation.
Hope that helps,
Reuben
