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Yes, it can be perceived as a problem that came from the Kubrick flash, but Kubrick has no chance to avoid it.
As I wrote, there is some connection between pcbID and serial (I don't know the exact way how to check if these two match or not). A reference to pcbID seems to be stored somewhere in the diags partition, thus flashing a diags image from a different device will always get the diags tools into inconsistent state when pcbID referenced from the diags partition does not match the serial.
The only way how to fix it would be to find the location of pcbId reference in diags and overwrite it with the genuine pcbId of your device.
AFAIK this inconsistency does not have any side effects besides problems with exiting the diags mode that can be worked around by methods I mentioned above.
None of my devices has any problems with registering and firmware updates.
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