Thank you for testing.

So when i load the graphics setup from within any GoG games folders, it wont work, however from the start menu they work fine.

for AitD1 at least the setup file is located here : "D:\Games\Alone in the Dark\Graphic mode setup.exe" GOGALONE1

what is that GOGALONE1 command that seems to be making it work?

I just tested, made a shortcut for the setup file and added GOGALONE1 to the command line, and it runs fine...very weird.

So i guess i will just put the shortcuts that the installer creates on the desktop, to the appropriate game folders, then i can run them from there.

That tells the Graphics setup program the game that's being set up.

It references registry values using that GOGALONE1...

Registry information: (64 bit)
HKEY_LOCAL_MACHINE\SOFTWARE\Wow6432Node\GOG.com\GOGALONE1

Yes, I think so. I agree that it does seem strange that they don't put a working shortcut inside the program folder itself.

Perhaps this thread and associated videos will help: http://www.gog.com/en/forum/general/the_ultimate_gogcom_dosbox_video_tutorial

Thank you for the help, I will look through them.

Create a games shortcut folder on your desktop; mine is not-so-creatively titled "Game launchers". Drag and drop the shortcuts into the folder. This all-but-eliminates that source of clutter on your desktop, and you'll always know where to find them.

Edit: I did the same thing with the manuals.

Edit 2: er, the two folders are actually on my D: drive, and I only put shortcuts to them on my desktop. You still just shift-drag and drop the game shortcuts into the folder shortcuts and they'll automagically be moved in the proper place on your D: drive.