I've done a little more investigation and this is certainly a macosx issue.
I can get it to work by...
editing eclipse/Eclipse.app/Contents/MacOS/eclipse.ini and putting the -data and -plugincustomization arguments into that file so it is now:
-startup
../../../plugins/org.eclipse.equinox.launcher_1.1.0.v20100507.jar
--launcher.library
../../../plugins/org.eclipse.equinox.launcher.carbon.macosx_1.1.1.R36x_v20100810
-showsplash
org.eclipse.platform
--launcher.XXMaxPermSize
256m
--launcher.defaultAction
openFile
-data
../../../../workspace
-plugincustomization
../../../../eclipse.preferences.ini
-vmargs
-Xms40m
-Xmx384m
-Xdock:icon=../Resources/Eclipse.icns
-XstartOnFirstThread
-Dorg.eclipse.swt.internal.carbon.smallFonts
and then I also changed the eclipse.preferences.ini file to change the path since it needs to be relative to the CWD for eclipse which is eclipse/Eclipse.app/Contents/MacOS
org.jboss.tools.jbpm/jBPM.Runtimes=jBPM runtime#../../../../runtime#true#
Now it works as it should.