Alex - I had no problem doing what you describe. Both namespaces load fine. 
I use an URLClassLoader to mimic what I think your code is doing.
I triped over a few things:
- first I got the alter-root wrong doing it from Java.
- I had to load clojure.lang.RT before clojure.lang.Compiler - otherwise 
you'll get an exception (loading ordering)

Could you put together a minimal running code on github maybe?

- Henrik

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