First off, there was a bug in the GiF reader making it shift the Y axis of the rectangle, so the image would actually have it's (0,0) shifted to (0, -height).
Secondly the writer would not error properly when the render window would be empty and would write junk. This has been fixed
Natron is better suited to work with media that retain original intent such as EXR. GIF support is more like a handy feature than one of the main features of Natron.