I am having a problem with an extended class as well.
When I step through the code, everything is going fine and the decoder (mx.rpc.xml::XMLDecoder) sees that the class is an extension and wants to get the values for the superclass first. When it gets into getApplicableValues(), it's looking for the values to be in the order of the definition which would be ok if the values collection didn't include the values from the subclass as well! It goes through the whole definition and doesn't find anything for the superclass because the values aren't where it expects them. When it pops back up to the subclass and starts to decode those values, it finds them because the definition order and values order match.
Is this a known issue? Or, am I misunderstanding something?
I found another thread in the forum about this same problem last year after I posted my question (hence the question about not starting a new thread back then). We had to re-work our classes to get things to work. I'm not sure why somone from Adobe has not posted something one way or another. Oh well.