I have an app that uses 256-bit AES encryption which is not supported by Java out of the box. I know to get this to function correctly I install the JCE unlimited strength j
For our application, we had a client server architecture and we only allowed decrypting/encrypting data in the server level. Hence the JCE files are only needed there.
We had another problem where we needed to update a security jar on the client machines, through JNLP, it overwrites the libraries in${java.home}/lib/security/ and the JVM on first run.
That made it work.