No, this seems to be an error. GraphML files created by yEd should work on any other system as well.
To provide adequate help, I need some more information:
Can you still open the file on the original system?
Are there any error messages when opening the file in yEd on Windows 7? If an error dialog shows, please use it's report button to send us a detailed error message.
If there is no error message, please send us a failing file.