I use yEd on Ubuntu 13.04, with executable jar package, and following java version:
java version "1.7.0_21"
OpenJDK Runtime Environment (IcedTea 2.3.9) (7u21-2.3.9-1ubuntu1)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)
I found that if I have another monitor attached (primary screen is laptop's LCD) and this monitor is rotated (has pivot), yEd positions its main window outside of visible area. There are also some problems with menus (sometimes they don't show up after clicking menu bar labels).