Sorry for not posting the code, as you said I felt I would be asking too much if I asked for it to be debugged
The problem was in the plumbing. The plumbing code executed, however, the junction didn't register any pipes. The problem was that I used the creationComplete event in the module mxml and in the ShellJunctionMediator I used the initialize event to detect module loading. So my moduleJunctionMediator was getting instantiated after the plumbing code executed.
After spending hours debugging I expected the error to be more... complicated. (sigh)
Anyway, thanks a lot for your help!