Having the same problem here. I was just making a change to the store message background, exact order of operations:
1) Clicked customize on the current theme.
2) Selected Images -> Store message background, changed image.
The new store message background displayed, but now the logo is failing to load again. Same error as before: http://www.webassist.com/forums/posts.php?id=32338
In summary, the reason is: "Once the logo gets set to a blank path, it wont be able to be updated, I have had our web master reset the f=default logo, you should be able to change it now."
Except I haven't set it to a blank path. A broken update statement somewhere in /home/cafecommerce/src?