Would it be possible for you to upload an example GraphML file (please remove all confidential information prior to uploading) and the corresponding EPS file? Otherwise it is hard to determine what is going wrong.
Please see How to upload files to yEd Q&A? for instructions on uploading files.
the GraphMl file and Eps file are added here.
thank youhttp://yed.yworks.com/support/qa/?qa=blob&qa_blobid=7112827641007534383
http://yed.yworks.com/support/qa/?qa=blob&qa_blobid=11589900335751661174