If you have more than 14 sites in the selection list, the bottom ones are hidden behind the 'visits by server time' on the dashboard page.
Suggest addition to common.css:
height:200px; overflow:scroll; width:150px;
...giving a scrolling list (width set so that long site names do not go off page edge, making scoll bar hidden.)
Keywords: site selection menu, css
Can you update to the latest Flash Player? Earlier versions had reported problems respecting z-order and wmode.
If that doesn't resolve the issue, please provide browser & Os version info.
In core/ViewDataTable/GenerateGraphHTML.php, try changing wmode from opaque to transparent.