Unfortunately I have no experience with these boards or what pncconf generates for them.
All I can offer is that these errors
Debug file information:
Can not find -sec MOT -var MOT -num 1
Can not find -sec IO -var IO -num 1
Can not find -sec LINUXCNC -var NML_FILE -num 1
Can not find -sec EMC -var NML_FILE -num 1
seem to relate to parsing of the .INI file not finding variables it expects at the various headings.
This one is strange Can not find -sec EMC -var NML_FILE -num 1
because if the line was not commented out LinuxCNC would throw multiple errors with any version >= 2.4
The second set of errors are tk/python errors, but also seem to relate to problems with the .ini file, either parsing it or even just finding it
set ininamearray($axisentry)
Don't know if this helps at all.
regards