I'm not sure if this is a problem with h5bp mobile or my version of ant or what - but whenever I run the build script on a project or even on a freshly downloaded version of h5bp mobile the js/lib files such as jquery and modernizr are not copied across to the publish folder. They DO appear in the intermediate folder so the build script is at least aware of them. It works fine on the non-mobile version for some reason.
Remove the included build directory and replace it with the newest one from github.
You need to update some properties in project.properties, though (JS libs directory, main css file, ..).