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I downloaded the Mind Map stencil, installed it in Library/Application Support/OmniGraffle/Stencils and restarted OmniGraffle. Upon doing so, the Mind Map stencil was at the top of the list, and clicking on it revealed the diagram shown on the GraffleTopia site. I dragged a rectangle around the contents of the stencil and dragged it to my blank diagram and ended up with the following:

To make it into a template, I did File->New Resource->New Template..., selected a blank diagram, then copied over the contents of the stencil and saved it in the Templates directory. Upon restarting OmniGraffle my new template showed up in the Miscellaneous category.

I'm no OmniGraffle wizard, could probably could the number of diagrams I've done without taking off my shoes, but this all seems like how I would expect it to work...what were you expecting?