I'm using yEd 3.10 with Java 1.7.0_09 on Ubuntu.
After saving a file which contains several rectangles stacked on top of each other with a group of SVG items on the very top, the SVG group is moved to the bottom level, thus being covered by the rectangles.
To better visualize the bug, I attached a sample file, which contains both a JPG screenshot of how it looked before closing the yEd graphml and a screenshot of how it looked after opening the file again, in case the also included graphml file doesn't have the same result as on my system.
http://www.filedump.net/index.php?pic=test1357225831.zip
In case more information is needed, please let me know.