First, some info :
To reproduce the bug :
It seems the display of characters is based on the bounding box of the character to display, but without the bold setting.
Would it be possible for you to upload a sample GraphML file that shows the problem?yEd does not offer a way to change the font weight for method names, thus I do not understand your second step in the reproduction instructions.
Unfortunately, this is a result if incorrect measuring of HTML text in Java's rendering framework. Thus there is very little that can be done about in yEd.However, there is a fairly easy workaround: add a non-breaking space at the end of your longest method name.