Siemens S25 X-axis counting error

Hi all, was wondering if you have any ideas on how to correct the problem we are encountering with our S25 machine. The machine is giving an X-axis counting error at gantry 1. I replaced the x-axis linear reader and the linear scale as well, but still getting the same problem. The machine cannot find the correct position of the PCB fiducials because the x axis is always off on the x position. Thanks for your help.

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