I recently updated to yEd 3.9.2 - thank you for PDF "automatic page settings". :o)
When exporting to PDF, there seem to be some rendering issues. Some Nodes/Elements arent rendered at all, most of them are only partly rendered. Tested with Adobe Reader 9.5.1 and evince 3.2.1 (Ubuntu 11.10, x64).
The issue seems to be related to color gradients.
SVG & PNG export work fine. Gnome image viewer, eog (v3.2.1, Ubuntu 11.10 x64), seems to have some issues with color gradients as well. Still, Firefox renders those SVG exports correctly.
Example .graphml & expots: