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I am having the same problem. I hadn't figured out the part where you could save it with the script if you did it by hand. I verified that does work, until you stop and restart OmniGraffle Pro 6. Then it can't save again.

If anyone has had any luck making this work again, please let me know. I also checked and OmniGraffle is running as me, and I have write permissions on the directory. Exporting by hand works fine every time.