I have an application where I try to load an external SWF. So, we have:
I don't think the issue is with your ScaleMode. There can only be one Stage per flash player. The "stage" property of your 'external' SWF references the Stage of your 'application' SWF after it's added to the display list. If the SWF is loaded and not added to the display list, the loaded SWF's 'stage' property will equal 'null'. Setting the stage scaleMode inside your external SWF won't dictate how it scales once loaded into another SWF.
Also, you're probably resizing the SWFContainer, not the SWF itself...thats why the SWF width and height properties are always 800x600. I'm not sure if this is what you're asking for, but from what I'm understanding, you may need to create a stage resize event listener.
Even with scaleContent set to "true" you still need to set an exact height and width to the SWFLoader control for it to even try resizing the internal SWF. All scaleContent does is instead of showing the SWF at regular or stretched sizes, it also up-scales the SWF if needed, and if not just scales it to retain the ratio of the original SWF.
Have you tried to use a scale effect on "External SWF"?
Scale Effect