I'm having the opposite problem in Fireworks that I was having in Dreamweaver...
In Dreamweaver, resizing a panel manually resizes the Flash app okay. When you resize the Flash app programatically, it does not resize the containing panel.
I came up with a hack to work around the Dreamweaver problem.
In Fireworks, resizing the Flash app resizes the panel just fine, but manually rsizing the panel does not cause the Flash app to resize to fit. I checked to see if I can get the correct geometry and fix it myself, and that does not seem like an option. CSXSInterface.getInstance().getWindowGeometry() returns the same results before and after resizing the panel.
The panels done by Adobe (i.e. Kuler and CS News) seem to have the same problem, so I am confident that I am not missing something... Right?
This is a pretty major problem with creating CS Extensions for Fireworks, and I see no workaround!