Thanks for the feedback. Be sure to tell your friends! ;)
By JRE directory, you mean you unpacked the zip file and put the two jar files in jre/lib/security?
Sometime it turns out that IDEs are not using the JRE we think... a good way to check this is to try running the example from the command line. Also in the chapter1 package you'll find a SimplePolicyTest class which will try a couple of things that check the policy files are in place.
What happens when you run chapter1.SimplePolicyTest? Do you find you get different behaviour using the command line versus JBuilder?