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Configuration files created attached.Please poke me in good direction.

More screen shots:
I don't understand where is the proper place in MesaCT to set XYZ axes PWM mode, assign pins for it, assign pins for respective encoders. Curious why in CT, under "Firmware' tab -> 'Mesaflash' tab: there is no options available - not possible to pick firmware file, not possible to verify existing one, 'Add firmware' not working (no reaction at all).

I know PID tuning will be from LinuxCNC but it's not starting at this stage.

For the third time with some more detail. To replicate
1. Install Linuxcnc 2.9.4 (rip should be fine but I used the ISO)
2. Install the Qtplasmac sim to the config folder
3. Open the sim to confirm its working
4. Close the sim
5. Install Linuxcnc 2.10 or run from another RIP folder
6. Open linuxcnc 2.10
7. Open the previously installed sim.
8. Upgrade message should be displayed
9. Repeat 6,7 The upgrade message will be displayed again and Linuxcnc exits without error message. 

I just wanted to test an upgrade from the 2.9.4 ISO to use 2.10 before asking a customer to upgrade his working system. I now know the workarounds but I don't think the bug will bite on a live system

FYI, I have just posted an upgrade script to go from 2.9.4 to 2.10 in the Installing Linuxcnc section that shows what I want to achieve. Becasue Linuxcnc does not maintain a buildbot on Linuxcnc.org, some changes to  the apt folders are required to point to the buildbot2 repo. We follow the Debian standards for APT in the ISO so there is some data in subfolders that needs removing.
Ref: forum.linuxcnc.org/9-installing-linuxcnc...n-2-10-master-branch