I found following error when I run clojure application as MS Windows service (via procrun from Apache Daemon project). When I tried to do 'require' during run-time, I got NullPointerException. This happened as baseLoader function from RT class returned null in such environment (the value of Thread.currentThread().getContextClassLoader()). (Although my app works fine when I run my application as standalone program, not as service).
This error was fixed by explicit setting of class loader with following code:

(.setContextClassLoader (Thread/currentThread) (java.lang.ClassLoader/getSystemClassLoader))

before any call to 'require'....

May be you need to modify 'baseLoader' function, so it will check is value of Thread.currentThread().getContextClassLoader() is null or not, and if null, then return value of java.lang.ClassLoader.getSystemClassLoader() ?