Hi,
This could be many things.
Not knowing the details of your task but thinking about your assertion about a 400 micron difference:
You will most likely have two different softwares being used, you will find that with the tracker, due to the type of instrument it is there will be quite a few options for aligning to the part i.e. creating the reference system. Check what the datum features are and whether they are common to both measurement systems and look at the files to make sure that the datum points are being held at the reference....this is the first check.
Unless you are using a probe attachment with the tracker you will not be able to measure features such as holes directly, if this is the case you need to manufacture tooling which can have variation but I would doubt 400 micron.
As per the advice from Hey Grandad, you could be looking at a scaling error, , with the CMM you may have a feature in the software which allows the user to input the CTE (Coefficient of Thermal Expansion) of the material and the measurement result will be adjusted to allow for the effects of any departure from the reference temperature. For the tracker, you will have an option to use the instrument reference as a scale which will either use the laser interferometer or the ADM (dependant on which tacker you have) but the reference is controlled by an instrument which is attached to the tracker and measures ambient temperature, atmospheric pressure and humidity. If this instrument is damaged or has been tampered with or is not calibrated then it can inject an incorrect correction.
Similarly to the CMM, the tracker can correct back to the reference temperature based upon the CTE of the material and the current temperature. Check what, if any, correction is being made.
Check if the tracker has passed its field checks, or whether they have been performed....Two face, ADM vs IFM, reflector check, the operators should be familiar with these terms.
There's lots of other things but please check these first, 400 micron is a lot, are you sure its not 40 micron? Easy to make this oversight, have done it myself many times!
Hope this helps.