This was finally identified after your post but before 2.0.1 release. The problem is that on Controller.removeCommand, there is no easy way to remove the associated observer in the View. Adding a removeObserver method in the View is a possibility. Considering that much of the sturm und drang
up to now in terms of bug fixes has been related to getting removeMediator to work properly the idea of refactoring it for this release was not attractive.
This issue is noted at the bottom of the release notes for 2.0.1:http://trac.puremvc.org/PureMVC_AS3/wiki/ReleaseNotes
* If you remove the Command for a given Notification name, then re-register any Command to that same Notification name, the new Command will be executed twice when that Notification is sent. This is because the Controller removes the Command from its commandMap, but currently has no way to remove the Observer from the Notification list because that is in the View, and there is no removeObserver method. Since this is an edge case, and would require refactoring of a particularly important section of the framework, it is being deferred until after the 2.0.1 release.