We're using this feature for the Pyret/Bootstrap-Snap! IDE integration, which is still in development and unreleased, but not quite in the way you showed, which is why we didn't notice this bug yet. But it should work, so I fixed it. Thanks!
I've since then added the new Lisp syntax for scripts, which I think serves the task at hand even better, so I'm personally not sure if we might not switch the script synchronization mechanism from xml over to lisp in the (near) future.