This is repeatable. I just installed the following version:
Product: OmniGrafflePro-5.1
Tag: OmniGraffle/5.1.1/final-137.11

I just need to create a blank document and try to save it to get the following message:
The document “Untitled” could not be saved as “test”. Cross-reference table doesn't end correctly.

Anyone knows how to fix this?
Thanks

Ziad