I can at least assure you that there isn't really an inherent problem with loaded modules. I'm currently working with an app that loads LOTS of modules; I have 55 modules loaded in a MultiCore Flex app in another tab of my browser as we speak, all connected with pipes and communicating cozily with each other.
Having looked over your code, I'd have to suggest that you either try to reproduce the problem in a simpler demo, or see where your modules differ from the ones in the demos here on the site from an instantiation and Facade initialization perspective.
Since there aren't any demos up right now that load modules, have a look at this excellent example, which also unloads the module and ensures garbage collection is working properly:
http://www.nutrixinteractive.com/blog/?p=132-=Cliff>