I never thought my 3d problems would exist in the CNC world as well. All my helically (?) drilled holes are consistently all 0.4mm too small. Is this something to be expected from a CNC during helical boring?
The Lowrider is designed to be more accurate than what you are seeing. Several issues could be causing your results. A few (but certainly not all) of the common things to look for:
Mechanical
- Grub screws on stepper motors loose
- Bearings in the core not seating snugly on rails
- Belt tension loose
Firmware
- Steps per mm not correct
Toolpaths
- Too aggressive, causing tool deflection
- Actual tool diameter much lower than nominal
Others here may offer better things to look for, but the things above are what come to mind at 4am…
Before coffee…
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It is special that it is always 0.4mm. That seems like it’s a setting.
What are your settings?
Do you use rough and fine machining?
Had same issue with helical drilling recently. Long story short, the 1/8" end mills i was using to make 1/4" holes were undersized. The shank was 3.18mm, but the cutting end was only 3.11 across the flutes. So, check you bits before you pull too much hair out! 
Used finishing pass also. Adjusted tool diameter in estlecam to the actual tool diameter and holes were perfect.
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FWIW, using the nominal diameter of 3.175mm in my CAM, I consistently got the “parts too big / holes too small” problems.
If I use a tool size of 3.00mm, I get a tight fit for parts and holes, but it fits, where it didn’t at all with the nominal setting.
It occurs to me that 0.4mm is really close to the error margin that I had. (0.35mm) at that, the fit of tabs/slots are still quite tight, so maybe I should be using 2.975 as a tool diameter in Estlcam…
I had very same problems, i found the soloution by cutting a 50mm square hole and a 50mm square to fit that hole, then measured x and y of both and found the hole slightly to small and the square slightly to big. I then tweaked bit size and repeated untill i got it correct.
If the steps/mm are correct and there is no other issue then the square you cut out should be bigger by the same amount as the hole is undersized.
If you find that the x and y of the square are different it suggests different tension on the belts or something is slipping (assuming the steps/mm are the same for x and y).