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The shape needs to be added to the graphics array of the layers array of the canvas:

Code:
OmniGraffleCanvas *mainCanvas = [canvases objectAtIndex:0];
OmniGraffleLayer *mainLayer = [[mainCanvas layers] objectAtIndex:0];
OmniGraffleShape *shape = [[[[omnigraffle classForScriptingClass:@"shape"] alloc] initWithProperties:props] autorelease];
[[mainLayer graphics] addObject:shape];