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I'm noticing a strange scaling issue with my machine. I've got my print head moving precisely 100mm when I tell it to in Repetier Host. But when I print a 100mm object, it's coming out 99.34mm.

20mm objects are coming out 19.54mm. So the scale isn't constant, which is the strange part.

Even stranger is that when printing out nophead's hole thing where holes are supposed to print out true to size, the 10.5mm hole is coming out 9.93mm! Which is WAY smaller than it's supposed to be..

What should I be checking?

I have delta_diag_rod to be at 267.8 and motion when moving around in RepHost looks spot on (checking with a steel rule on the bed and moving in known increments).

Adjusting delta_diag_rod to print perfect 20mm boxes unsurprisingly prints out oversized 100mm objects. What could be wrong here?

I think you're just noticing how plastic shrinks when it cools. As long as your XYZ steps per mm are correct (different between the 15 and 20 tooth pulleys), I would just recommend making your parts about 1% oversize with your slicer program.

verify your extrusion width but your not going to get everything perfect, plastic shrinks.
You're better off calibrating on the larger object.
The only really accurate way to calibrate is with a dial gauge mounted to measure axis motion and set the motion scale that way, it's something of a pain to do on the rostock, sine the gauge has to be mounted accurately and that's hard to guarantee with the geometry.
I have done that sort of calibration on more traditional printers and every single one prints about a 19.8-19.9mm 20mm cube.
Circles tend to shrink, see Nopheads post on PolyHoles for a good explanation why, basically you are stretching the plastic around the hole, and that tension guarantees additional shrinkage.

I did read nopheads blogpost about hole shrinkage, but his thingiverse object is supposed to compensate for it. But my holes are coming out waay undersized.

I forgot to mention that extrusion width has been verified and gcode was checked too and looks correct. Gcode tells the print head to move the dimension length minus the extrusion width.

Ill try to calibrate to the longer 100mm object.

The circle thing doesnt compute in my head..