John,
I am trying to do something similar, using BouncyCastle to do PGP encryption, and EDT for FTP stuff.  Each is a separate Web Service deployed on the same server in Tomcat.  Whenever I run the PGP Web Service, subsequent runs of my FTP Web Service fail with java.lang.reflect.InvocationTargetException.  I have to restart Tomcat in order to run any FTP jobs after a PGP job.  It would seem that the classpath is becoming corrupted somehow.
Have you run into this?  Any ideas?
Thanks