But it does seem like this is the problem so for the time being I may have to give up trying to build with Leiningen.
If you know what your dependency set is for the time being, you could always go the *really* ugly way and create your *own*, pre-merged *Metadata files and ensure they're the ones that get packaged in your final über-JAR..?
ap PS: It hurt a little to write that, but it should work... ;-)