RT.baseLoader assumes Compiler.getClass.getClassLoader will return a sane value. If Clojure is placed on the bootclasspath, it will return null.
Relying on baseLoader less may be possible; it looks like the ClassLoader/getSystemResource static method may get us the access we need to the bootstrap classloader, which would solve the problem I first noticed with using RT.load with the bootstrap classloader. However, there may be other issues beyond this.
I plan on investigating this further, but I've created this ticket to explain what I've discovered so far for posterity, etc.
Note that placing Clojure on the bootclasspath cuts its startup time in half; it's a measure that Charles Nutter of the JRuby project recommends.