Thanks for the feedback. I did set the entire games rooms and cameras to 64x64 pixels with only the size of the viewport being set to 704x704 so it wasn't a tiny square on the screen. It seems as though that was not enough as Gamemaker seems to do some hokey pokey business. That's my bad (doh!).
I checked the resizing of the application surface and I can now see the end effect makes more sense, honestly I don't know how I didn't realize during development, woops... I will release an update with just this patch after the voting ends with the fix for this.