I’ve found the problem lies in the way the theme mod option is saved – have a look at the source, you will see the URL is stripped of some characters ( : . / ) and it’s one big long string with no path separators – for example, my logo gets output as:
https://httplocalhostsite-namewp-contentuploads201503site-name-splash_01png
So it seems there’s some kind of problem saving the value in the options.
This seems to work if you go through the ‘Appearance > Theme options’ instead of ‘Appearance > Customise’
Hope it helps ??