OK, since I cannot replicate this, nor figure out the reason for it, we have one of two options:
- I keep doing some random tests, that are not guaranteed to fix the problem, and keep posting them here with you testing to see whether they have any effect.
- If you are comfortable with it, dm a metadata.db file of a library that have this problem. You can copy it to separate folder, open it with calibre, and delete all the book records before sending it.
It is your call.