Apologies for this broken functionality, I have just committed version 0.2.3 which should solve the problem of the additional calendars not being displayed.
Whilst investigating, I also discovered that the database upgrade script wasn't quite right and may have caused issues for anyone upgrading from an older version of the plugin and trying to save dates for multiple calendars.
Please also note that the way to define which calendar is shown is now as follows and described in the FAQs:
Using the shortcode
[availability calendar="calendar-id"] will display the calendar created with ID
Hopefully this resolves the issues, if not please get back to me and I will try dedicate the time to fixing things.