Unfortunately, old versions of yEd are no longer available.
However, the current version of yEd should be backwards compatible with all 2011 versions. Therefore, I would be grateful if you could upload your file here so I can investigate the problem. Please do so only if the file does not contain any sensitive data (this being a public forum). See How to upload files to yEd Q&A? for instructions on uploading files.
--- Edit ---
Thank you very much for uploading the problematic GraphML file (and reference screenshots). The file in question was *not* created with yEd, but with Graphity. Although both applications use the same file type, yEd cannot correctly display Graphity generated GraphML and vice versa.
The good news is, when you open your file in Graphity, it will look as expected.