Yep, that seemed to work. I don't know how I missed that config option, I was looking specifically for it.

And the 6550 is a holdover for when I was too poor for a graphics card.

Thanks for trying. Since then I have tried to run in 640x480 mode and in all the compatibility modes and nothing has helped.

I'm really not sure what to do at this point.

Here is some more information on my graphics if it helps:
(my graphics card drivers are up to date)

Yes, I have. When I right click it just brings the 30x30 pixel block to the front. That was the first thing I tried.

My game starts as a ~30x30 pixel square at the top left corner of my screen. I tried switching the graphics mode to simple in the config, but that had no effect. I am running windows 7. (don't mind the changing background)