Hurrah!
CALM does not eat the alphabetically first three libraries any more! But only when putting in manually. Via "Load All Libraries" still I get the three bogus libraries 00,01,02 and the alphabetically first three real libraries do not appear.
I also get still the other error I reported in my last post as well: Whenever clicking "Get All Source Library…" on the third tab CALM throws the following error message:
calibre, version 2.63.0
ERROR: CALM Target Database Connection Attachment Path Error: CantOpenError: unable to open database: /users/peterb/documents/meine/ calibre-books/duk/metadata.db
More detail about this error I have reported in my last post.