Thanks all for the help.
bluepeter, thx for the link - I did not end up doing this and instead manually mucked about with the KoboReader.sqlite file. All of the bogus entries were the first ~1000 entries in the content database, conveniently - deleting them seemed to have fixed the problem.
Sirtel, interestingly, both commas and semicolons as separators seem to have the same behavior. Unfortunately this behavior is still unpleasant and incorrect... the "John issue still occurs. I am going to try and investigate further.
John F, deleting the book on the Kobo device through the UI and re-transferring worked. All of my metadata issues did appear to be consistently caused by having extraneous XMP metadata on books (excluding one PDF which turned out to be corrupted): the presence of such means that Kobo may or may not read the standard author/title metadata.
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