Found the problem. In JDOConfLoader in the getDatabase() it calls
loadConfiguration(source, whatever) each time and reloads the file, or
tries to at least. The problem being that if the JDOConfFactory is
used, there is no file to reload, and its null (hence the problem).

Using the Castor-0.9.7 relase I just added the line 
if(_jdoConf == null){
    ....
}
at top of that particular loadConfiguration method. Anyone see this as
a problem? Or has it already been fixed?

-Nick

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