I've tried clicking "Clear cached data" in Performance settings, and also running "drush cc all", but some cache tables always have some rows left in them:
I want to completely empty all my cache tables before I take a db dump and transfer it from my development box to my production server.
I'm not in depth familiar with those cache tables. But the most obvious reason would be that the cache is created after the cache is cleared.
To solve your problem you could manually delete the content in the tables with drush or some other tool to connect to your database. You could also leave out the contents of those tables, like the backup migrate does by default with all cache tables, watchdog etc.