If you ever need to access FlashVars from a MovieClip that you loaded externally, make sure it has been added to the stage first.  If it hasn't been added you can access any of the variables.  This isn't a problem with the loading/root clip because the document class is granted immediately access since it is the stage.

I usually don't have this problem except I was using a 3rd party framework that didn't wait for the ADDED_TO_STAGE or COMPLETE events before accessing those variables.