How an SVG file is displayed always depends on the application that displays the SVG almost as much as the actual SVG definition. In other words, this might be a problem of the application you use to view your SVGs. Usually, the easiest way to determine if the problem lies with the SVG definition or with the application displaying the SVG is to open the SVG in different SVG viewer application that use independent SVG frameworks. E.g. I usually compare Google Chrome, Mozilla Firefox, GNU Emacs, and Apache Batik Squiggle. If all of these display the SVG in the same way, it makes sense to look for a problem in the SVG definition. Otherwise the problem lies with the viewer application.
In any case, without the actual SVG file (and the corresponding GraphML file) I cannot tell you where the problem lies. If you decide to upload the SVG and the GraphML here (see How to upload files to yEd Q&A? for related information), I will try to look into the problem.
What application were you using to view your SVG?
