So there's still something wrong with the XML cache DB. I thought that starting with "-cc" (cache clear) would fix that, but it apparently can't reset the DB (= drop tables & indexes) when the DB file is somehow corrupt. I dunno what might have caused it, but I doubt it has something to do with switching to the newer MAME version. You could however remove the DB file completely so it will be recreated from scratch during the next start-up ("rm ~/Library/Application Support/qmc2/mame-xml-cache.db").
Oh, and since your "machine list DB" file also seems to be corrupt, please remove that as well
("rm ~/Library/Application Support/qmc2/mame-machine-list.db").