Just before the change I used the Packaging Configurations to check a value and it worked fine. After I updated I tried to select the 'packaging configuration' menu and got a popup eclipse error:
Could Not Accept Changes The currently displayed page contains invalid values.
I moved the packaging-build.xml away in case there was a problem with it, but I still get the same error.
So I tried to edit the packaging-build.xml file, but whenever I use "run packaging" it overwrites my changes with what was in there before I updated to RC2, and if I make it read-only packaging won't run at all.