David, this happens when a user has a single image directory with multiple project files, like ab_Minimal.jap, ab_Neptune.jap, and ab_Tiger.jap. The core gets confused because the upload path is stored in .info, not in the project file. So, even though there are three different project files, there's only one .info file sitting in the image directory.
So David, there is an easy fix: just use the remoteDirectory string in the project file to compose the upload path, instead of the upload path in the .info folder.