yEd relys on the printer services made available by the Java runtime and I'm not sure whether there is anything we can do to solve this problem in yEd. This may be a problem in the interaction of your printer's driver and Java.
This blog post
describes the same problem with another application. The suggested solution is a complete removal and re-installation of the printer driver. In any case, please make sure that you're using the latest drivers for your printer and the current Java Runtime Environment (http://www.java.com).
As work-around, I propose to export the diagram to an image or to PDF and print this with another application. Alternatively, you can check if printing to a PDF printer like PDFCreator works.