What I did to deal with this (and I'm not 100% sure that it is 100% correct, TFS is an unpleasant complex beast).
You need to edit the task workflow: in Visual Studio, go to tools | process editor | Working View Types | Open WIT from the server. Select "Task" and edit the layout for new states with appropriate transitions. Save this (no, it is not obvious - just right-click on the tab in VS).
then export the general configuration:
witadmin exportcommonprocessconfig /collection:http://myserver:8080/tfs /p:"Test" /f:"CommonConfiguration.xml"
edit it as you did, and import the configuration back to the server:
witadmin importcommonprocessconfig /collection:http://myserver:8080/tfs /p:"Test" /f:"CommonConfiguration.xml"
If you use TFS Power Tools, you can update them in Visual Studio to save as a template, the general configuration is the tab in ProcessTemplate.xml
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