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Thanks for the replies, but some misunderstanding here.
The system is fine, up and running LinuxCNC 2.9.3, configured for the X-axis with joint0 and joint1 as it should be (cutting a big slab of 5 mm Alu while I am typing this). The only thing I am adding is a racking detector (for which I use encoder_ratio looking for a mismatch on encoder disks on both X axis).

While browsing through the HAL functions I ran into Matrixkins, and I wondered if this is not an easier way than changing some HAL values to square the axes. Since it does not apply to a tandem axis, I'll drop the issue.
But thanks for the replies anyway.

Robert

Yes.
When mounted inside, the encoder wires have to go inside, and those are the ones most susceptible to interference.

No need, since 2.8 the joint/axis is implemented in LinuxCNC, so just choose "tandem joint/axis" in the wizard.