There are 13 KEGG mol files that cxcalc's majorms plugin considered to be "Inconsistent molecular structure".
I was able to use msketch's StructureChecker to correct all of them as best as I could, and subsequently, these worked fine:
The first three in the previous list (C00282, C12393, and C12394) are the ones that I wanted to post about, because StructureChecker said that they were valid, and either had no errors, or successfully corrected all errors. However, when I ran the saved files against the cxcalc's majorms plugin, I still got an "Inconsistent molecular structure"
I repeat, this contradiction only appeared for C00282, C12393, and C12394. The other four files had valences that could not be corrected automatically.