With the new version there is now a big difference: After saving the three library names 00,01,02 do not appear any more. But of the 5 libraries I had put in and checked, two remained in the window, but CALM is correctly reporting that currently 5 libraries are checked. These two that remained are considered for the consolidation process.
But I never got a situation like your
second screenshot. I always get a situation after saving similar as in your
first screenshot. My saving reduces my selected files from 5 to 2 (there is always a reduction of 3, has maybe to do with 00,01,02?).
I attached the new .json file for your inspection.
I'll come back tomorrow, here in Austria it is already after midnight.