First question, where did you get your mouse-bites? Some have drawings on the edge cuts layer, some don't. Either way, you need to make sure the outline is a continuous line, otherwise the 3D viewer gets confused. You can ignore the 3D viewer, it's inconvenient but doesn't affect the gerbers.
I think there are problems with that site, it didn't work correctly on some files I uploaded. It's a neat idea turning the gerbers into a 3D view, I've seen one that also displays components.
That looks like a problem with inch/mm conversion, or number of decimals in the gerbers. I am sure we have seen that before, I don't remember the fix.
I followed the guidelines at http://www.sl-alex.com.ua/en/page/kicad-preparing-pcb-for-seeedstudio and the board looked ok in the Seeedstudio gerber viewer, but that was with a "simple" outline (no slots).