Apple,
If I’m not mistaken when you setup your plugin development workbench you need to disable the MyEclipse plugins as you certain don’t need them for plugin development. This will avoid the conflict between the two workbenches.
The alternative work around (to avoid conflicts with our license manager) is to start both copies of Eclipse up and leave them up. If you need to restart one, you need to restart both otherwise the license manager will issue you a warning when you restart the 2nd workbench (it sees it as a 3rd install of the same license).