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:
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Can you still open the file on the original system?
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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.
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If there is no error message, please send us a failing file.