A simple test.
Find the peak position for an element.
Move 5mm to either side and then back to the peak position and do a 10 second count. Go +5, pk, -5, pk, etc. repeat 5 times.
If counts are consistent try +-10mm and +-20mm. 
If not, then clearly a reproducibility problem.

As a microprobe specialist, I would have spent at least 2 days or more dialing in that spectrometer for linearity and reproducibility.
Not uncommon to spend a week trying to find the one little thing that screws up reproducibility.
Nearly impossible to do the job correctly in less time.

Cyril

> On Sep 4, 2018, at 3:34 AM, Deon van Niekerk <[log in to unmask]> wrote:
> 
> Hi Cyril,
> 
> The engineer is from a company that represents JEOL here, but not a JEOL employee. I was using the down time to get some admin, etc. done, so wasn't looking over his shoulder the whole time....I assume he checked the linearity and reproducability during spectrometer calibration. He did fill out a JEOL service repair report and did do spectrometer calibration and xtal optimization. (I was hoping that he would return to fix the problem under a workmanship guarantee, but they wants to put it down as new labor on our service contract, which I'm not happy about).
> 
> Thanks,
> Deon.
> 
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