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What you're seeing is probably an issue of long-standing problems with window focus in the Eclipse-based client. It will get fixed if enough people complain about it. But writing about it here doesn't count; there need to be customer support incidents for the people who set priorities to pay attention.
Meanwhile, I think you will have fewer problems if you close the Designer and/or Administrator client before you start debugging. Most of the confusion comes about when switching focus between these windows.
Feedback response number AGUD8AZLD5 created by ~Julia Prefootherlen on 11/08/2010