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I just tried that and it doesn't work. I did it twice to make sure I didn't screw anything up.

File:New Resource:New Template
Hit New Template Button
Get a blank, portrait document
File:Page Setup:Landscape:Okay
File:Save
Set name to Blank Landscape
Omnigraffle:Preferences:Default Template
Choose Blank Landscape as default
Okay
File:New
Tada! A blank, portrait document. Oops. Okay, I guess I'll continue to manually change this every time I start a new document.