If you could attach the project I'll take a look.
Sorry Jeff, this issue seemed to drop off my radar due to an extended Christmas break
I was able to reproduce your original issue - its nothing to do with the condition, any change that causes a save to the choreography results in the namespaces being messed up. I have also tried out the most recent BPMN2 editor, and it still does not correctly retain the fully qualified name of the message types.
Will get back to you when I know more .....