Message4617

This is due to the change in
http://fisheye3.atlassian.com/changelog/jython?cs=6260

The fix tried to make registry file properties overridable with System 
properties (e.g. -D options to the JVM), which is IMHO correct.
But it lead to the behaviour change you describe. 

Roughly speaking, properties from (any) registry file only are added if 
not yet present. So my first idea is to read those of the user file 
first, and the installed one second.
This would hopefully revert the behaviour as you expected so far (before 
beta 4).

I'll put together a snapshot build for testing it out.