Sorry you're having trouble here. I’m not sure why there's such a discrepancy in the exported file.
If you can email us at
omnigraffle@omnigroup.com with the Graffle file in question, we can attempt to figure out what's happening.
A note: While we do attempt to monitor the forums, they're primarily a user-to-user resource. For the quickest response, it's generally best to contact us via email.