I noticed in the source code when I inspected the logo directly that it was pulling the retina logo (I am using a MacBook Pro 15″ 2016, which has a Retina display), which I hadn’t replaced in the logo options. I added it, and voila it fixed itself!
It might be good to put in your documentation that if the logo doesn’t change it could be because one is viewing on a retina enabled device.
Thanks for your help! I wouldn’t have thought to inspect it without you. 🙂