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Yeah it's the slicer not compensating for extrusion width. A common problem with 3D Printing. Skeinforge supports a feature I think it's called Widen which compensates for hole size and such. I personally use KISSlicer which does a fantastic job. When I design a hole at 3mm it prints 3mm. (so to answer your question yes I design the holes to the exact spec. The trapped nut holes are designed to have clearance for the nut, but only about half a mm or so)

I'll upload the Sketchup files later tonight if I can find time :) so you can adjust if needed.

Thanks for the heads up!