I have WPMU 3.3.2 with Atahualpa 3.6.7.
When I upload atahualpa_header_1.jpg and place %image in ATO>Style & Edit HEADER AREA>Configure header Area, the header comes up fine. If I delete the image from my media library and then upload a different atahualpa_header_1.jpg, the site retains the original image. I have had this problem in the past, but if I removed %image and deleted atahualpa_header_1.jpg and then started over, I eventually would get the new header.
However in this latest site, I have followed the usual work around, but if you reload the page, eventually the old header comes back and if you keep reloading, eventually the new one comes back and then they will start alternating with reloads.
Here is the URL to the site. http://sophia.smith.edu/betablog/imagingcenter/