I've encountered a similar problem when loading a Flex SWF into Flash. The Spark dropdowns were being offset in an incorrect fashion.
I've managed to devise a solution that, while it's not perfect, is effective in my case.
I've created a Custom DropDownListSkin and applied that as the skin when adding the dropdowns. You can find the basic code here
In the code you'll see a section called <s:PopUpAnchor id="popUp" etc.
You will need to also create an as3 class that extends PopUpAnchor. Within this class you will need to override the function calculatePopUpPosition. Here's the code that I used, I hope this is of some help to you:
override protected function calculatePopUpPosition():Point
var globalPoint:Point = this.localToGlobal(new Point(0,0));
What's happening here is that I'm getting the global position of the dropdown and applying the coordinates to the dropdown that I'm using
Thanks for the help. I had gotten as far as PopUpAnchor when I gave up before.
As it turns out, the compiler setting for MarshallingSupport finally worked. I have no idea what was wrong, but the other projects finally got so they would compile with MarshallingSupport included. It might have been something as minor as the other teams not running "clean project". I don't know. It works now; I'm happy.