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Without the file to inspect, it's hard to say whether you're running into a bug or not, but one way to test would be to select the elements near the exported white space and see if the bounding box leaks over the page boundary.

One possible fix would be to set the "Export Area" to "Specific Region" when exporting so it only exports the area bounded by the page. I hope that helps!

If you're still running into trouble, feel free to email our Support Humans at omnigraffle@omnigroup.com.