Using Flex Builder brought me to a frustrating problem.
As soon as my application got a vertical scrollbar a (about 50px high) margin appeared above the scrollbar and all content was moved down. It was still flash content up there – so not the flash itself was moved down – but it was not used for any controls.
Working on this and circling around it brought me to the strange solution. One of my controls had the ID-attribute value „controlBar“ (at first it was an mx:ApplicationControlBar with that ID till i changed it to a canvas or button for testing later). When I changed that id to „controlBar2“ everything was fine again.
Maybe Ids with the same name as a class/component are not allowed, but I don’t know for sure, yet.
So keep an eye on your component Ids in Adobe Flex 3.