Could you post your sample project so that we can have a look? Is the issue only with popUps or with the entire module?
Sorry i did not see that you had answered at this time.
I resolved my problem since that time.
In fact the skin class was not compiled with the top level applicaton since the component was only used in module.
passing the moduleFactory attribute i resolved the problem.
However moduleFactory is not bindable, and that force us to manualy setting it (for example on creationComplete).
A cool feature would be a "autoDetectModueFactory" attribute that would make the PopupWarper getting the factory from the parent mxml component automaticly.
Best to file this as a feature request on the popup library in our bugbase.