I am also having trouble making pixel-perfect output, but it seems to be a problem with strokes but not fills. This first image is a screen capture of the canvas from my OmniGraffle editing window, where I have created a canvas 20pt by 10pt. The object on the left has a 2pt stroke, the one on the right has no stroke. As you can see, the tops and bottoms of these two objects are aligned.
When I output the canvas area only to PDF at 100%, 72 pt/in, and view the resulting PDF file in Preview, the fill-only box on the right is pixel-perfect, but the stroke on the left appears to be offset down and to the right by perhaps one half pixel. The tops and bottoms of the two objects in the PDF file are not aligned, and you can clearly see that the PDF image is in fact not identical to the image as seen in the OmniGraffle editor.
Is this a bug, is the stroke supposed to be offset differently in the PDF output than in the OmniGraffle editing window, or is there a way for me to control this behavior? I suspect this same effect is happening in my PNG file outputs, as I am getting aliasing artifacts for strokes but not plain fills.