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I think I may have resolved this, I modified the properties directly in .java/deployment/deployment.properties file and also set a system properties in /etc/.java. I noticed in the user file that there was a reference too two jre installations. This would appear to have been caused by a reference to a previous install of the 64-bit JDK with the same version number as the 32-bit JDK, the 64-bit installation was removed by yum erase.
In any case setting the jre arguments in the properties file means they appear in ControlPanel and that I can now connect to he plugin for debugging in netbeans. However, I have not tried modifying the jre parameters from control panel which was the original 'symptom'.