I know it is 2 years later, but I'm also getting this error also, with the exact symptoms. Has anyone resolved this, or have any idea what we might be doing wrong?
Same problem. It didn't occur with the same project using the initial Flash Builder release. It started with an update to Flash Builder version 4.0.1 (277662)
My specific error refers to my module, DataSystemModule:
Unable to resolve a class for factoryClass: st_core_datasystem_DataSystemModule_mx_core_FlexModuleFactory.
Generally speaking (for the search engines), the error is:
Unable to resolve a class for factoryClass: [classname] _mx_core_FlexModuleFactory
I've found that if I perform a project clean, the problem goes away for a little while.
Just wanted to follow-up. After adding classes and code to my project this directive, -generate-frame-loader=true, has lost its effectiveness and the error is occuring with increased frequency. So, as frustrating as it is the only work-around is to clean the project, over, and over, and over again.