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Topic: Calibration: Outer dimensions vs inner dimensions

I'm calibrating using this:
http://www.thingiverse.com/thing:28109

Actually I'm finding that with 88/88 (SD defaults) for EEProm steps per MM on the X/Y I'm getting almost exactly 110mm each way when measured with calipers. I'm getting more precisely 110.20 on the Y and 110.41 on the X. But still pretty good I think.

Problem is, the inner boxers are supposed to be 10mm x 10mm and I'm only getting 8.90mm x 9.01mm. What's wrong?

If I adjust my EEProm steps per MM to get 10mm x 10mm on the inner boxes, then my outer dimensions are too large.

My SD3:  Clear plexiglass case, case heater, X axis stabilizer, Z axis stabilizer, thumb screws, filament guide, heatsinks on all motors, extruder fan, controller fan, heatsinks on motherboard, Y rod pillow block, USB and Power on/off switch, fully calibrated including trimpot tuning. Am I missing anything?