The failing files are inside ZIP-archive. That fully explains all the failures you see. I'm quite certain these files have never been tagged with TagScanner either, it's just a special feature of foobar2000 that it can play and show these without manually extracting them first.
You should either remove the zip archives from your music collection or change your exclusion filter from "*.CUE" to "*.CUE;*.ZIP".
I changed the exclusion filter to "*.CUE;*.ZIP". Formerly I had only *.cue, without quotation marks and lower-case letters.
Most music files I own were ripped from CDs, using EAC. Not extracted from zip files. And zip files, in case they were present, were excluded from the folder containing each album. I use two HDDs. After tagging each album in the first HDD with TagScanner I copy it to the second HDD. I did this with each album. It was a more than a year work.
After changing the exclusion filter, I closed fb2k, open it again and I didn't find differences.