CURRENTLY is this for new WebObjects and Wonder applications:
<woapplication name="${build.app.name}" frameworksBaseURL="/WebObjects/${project.name}.woa/Frameworks"

SHOULD BE THIS:
<woapplication name="${build.app.name}" frameworksBaseURL="/WebObjects/${build.app.name}.woa/Frameworks"

project.name needs to be replaced with build.app.name, otherwise a custom build.app.name that is different to project.name will result in a non-working frameworksBaseURL that does not correspond to the custom name that applies to the woa bundle (both app and split bundles have the desired custom bundle name)