Edit: Deleting the yEd profile directory /Users/[USERNAME]/Library/yWorks/yEd solves this problem (see the comments below).
What Java version is on your Mac? (You can see the Java version yEd is running on in the Help > About dialog.)
It is possible that the Java installation didn't complete properly, and the Java runtime is corrupted. Maybe a re-install already fixes your problem.
my version is 1.6.0_29 (Apple version) and there are no updates available from Apples homepage.
Kind regards,
Stephan