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Do you know what version of visio created the file? I ask because Visio 2010 and Visio 2007, both use .VSD, but have big differences. So much so that a Visio 2010 VSD won't open correctly in Visio 2007 app.

I'd expect that if the VSD was created with Visio 2010, then importing it to OG's going to have problems.

One work around would be use Visio app to create a PDF, and then open it in Omnigraffle. If you don't actually have Visio, then install the Visio Viewer.