I loaded your ISBoxer profile up, just changing what game it was using. Then I used the hotkey you set up to make the VideoFX.
Here is the source:
Note that the source covers from the silver leaves in the top left corner to the roof of the house in the bottom-right. It's aspect ratio (width/height) is ~1.51.
Here is the viewer, both with and without the ISBoxer Control Panel open. Note that I have left the ISBoxer Control Panel open for Slot 2 so you can see the source location.
Note that it is not treating the source like it is at 0,0. The top left corner of the source is in the correct place (those silver leaves). However, you do see some parts of the source window below what you might expect (character's legs here) because the aspect ratios of the source and viewer do not match. Source: 1.51, Viewer: 0.83.
VideoFX always match the aspect ratio of what is seen of the source to the viewer. They can't scale independently in both dimensions. If for some reason you can't change your viewer to have the same aspect ratio as the source, this is a limitation you'll have to live with for now. You can both scale up and scale down a source as long as the aspect ratio of the viewer matches.
If the above does not match what you are seeing, I don't know what is going on I'm afraid.