I have a site that uses a MasterPage... I noticed that on the web pages that use this MasterPage, I have no control of where the content is placed. For instance, I have several labels that I don't want at the absolute top of the Content Placeholder, but about 1 inch down from the top. In every case, they are at the top of the Content Placeholder, not 1 inch below the top.
Place a 1x1 pixel transparent image (or use the blank.gif that DHE placed in "Files" map) in the upper left corner of your webpage. Then you will see all your content be placed where you want it.
You are right, the top is calculated as the top of the upper object found in the page; a good tip is the one Petran said, add an hotspot on the top ;-)