I believe I've re-discovered the issue reported here http://swizframework.jira.com/browse/SWIZ-24
When a popup is created in a Module and added via PopupManager, the swiz instance that processes the popup is not the module instance, but the "root" swiz instance of the application.
When the popup in question is not a type included in the root application, the root swiz instance can't handle it and we get a runtime error:
ReferenceError: Error #1065: Variable foo is not defined.
at flash.system::ApplicationDomain/getDefinition()
A workaround is to include a dummy variable in the root application of the popup's type.