Thanks for the help! I am truly stumped.
I am using paint.net to create my images. I have used a plugin to optimise my images for web use but I still get the same result. I have noticed (after trying nearly every .png image I have in Spine) that nothing seems to make a difference. I have tried images with and without a transparent background, big and small canvas sizes. The size of the file doesn't seem too important either.
Although some work, most of my recent images don't. I think it is related to paint.net as my older images were created with a variety of odd little image editors built in to game dev kits. Saying that my backgrounds were all created in paint.net and work fine.