Items are all the wrong size!

I have my machine very much fine tuned to within a few thou… How ever when i cut out a square slotted piece of plexi that is supposed to be 1x2 it is undersized by an inconsistent amount to the slot size and some depth sizes.

It is definitely on the correct toolpaths.
Im using the right bit size.
The Machine moves very accurately and repeatably in x and y and z.
Any Ideas?

Calibrate the machine for effective endmill diameter / runout.

See http://www.shapeoko.com/wiki/index.php/Calibration_and_Squaring_the_Machine#Runout and the following section.

Not understanding… what am i missing?

Yes i did. And @PhilJohnson i will slow her down see what happens.

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I have found when cutting plexi as phil said slow and shallow. The problem is as the bit heats up it can deform the plexi. On top of this if you can slow down your spindle that will help. In addition swap out your bit for a single flute bit. This decreases the amount of temperature you will get. In addition to this remember if you see the plexi sticking to the endmil it will cause a deformed cut. One last additional thing I have not played with much but might help would be to cut the shape offset a little large. Then do a final pass with the size you want this would decrease the amount of material you are cutting and would help control that heat.

I use a calculator to help with FS. And so far it has not let me down.
With plexi i use a 2 flute as 1 flutes dont bottom out.
I go at nearly 75ipm speed 1 and doc of .05