Apologies for slow reply. I just had two unrelated but, in combination, major hardware problems that have led to me having to set up a new Media PC and make a clean MC install on it, and then build the library again.
From the detailed report by MC after the library import, it would not import around 2,500 files (roughly 2.5% of the whole), almost all flac but some jpg files too, and - interestingly - almost all the rejects were from a single genre folder. (my storage folder scheme is Genre/Artist/Album). Everything else is working fine, so at least I can listen to most of the music again.
The rejects include the files which the old library was giving the error message on. Random testing shows all the rejects will play with other programs, so logically this is some sort of issue with MC, or else an issue of MC being abnormally sensitive to something which other players can take in their stride.
I am going to try some filename changing on a few folders, then see if that makes a difference, then some tag changes, (thanks for your suggestion BBB) then if that doesn't help either, overwriting some folders from a back up, and then if necessary from an older back, up to see if I can pinpoint some corruption issue.
I will report back later, as and when I get somewhere, but any additional comment gratefully received in the meantime.