Sorry, same error. But with some additional information.
- CALM still eats the first three libraries. I' ve written them in manually.
- CALM still produces three bogus libraries at the end with "Load All Libraries" *and* the first three libraries (alphabetically) do not appear. (as before)
- There is now an additional issue: Clicking "Get All Source Libraries/Custom Column Combinations" an error message appears.
This error message appears as many times as libraries are left: E.g. when saving 8 libraries - 3 eaten = 5 libraries than the error messages appear 5 times after pressing 'OK' then CALM displays the text which appears after pressing "List Current Source Library".
I always deleted folder, quit, deleted the .json file, restarted.
Another tiny issue: If a user (me

) presses "Delete the Entire CALM Library Directory" *before* one was created, then no message window explaining the wrong actions appears but an error message about an unhandled exception.
Spoiler:
calibre, version 2.63.0
ERROR: Unhandled exception: <b>AttributeError</b>:'CALMTargetTab' object has no attribute 'target_db_full_path'
calibre 2.63 embedded-python: True is64bit: True
Darwin-14.5.0-x86_64-i386-64bit Darwin ('64bit', '')
('Darwin', '14.5.0', 'Darwin Kernel Version 14.5.0: Thu Jun 16 19:58:21 PDT 2016; root:xnu-2782.50.4~1/RELEASE_X86_64')
Python 2.7.11
OSX: ('10.10.5', ('', '', ''), 'x86_64')
Successfully initialized third party plugins: DeDRM (6, 4, 3) && Quick Preferences (1, 4, 1) && Quality Check (1, 9, 11) && EpubMerge (2, 0, 12) && Search The Internet (1, 7, 6) && Goodreads Sync (1, 9, 1) && Import List (1, 1, 5) && Favourites Menu (1, 0, 4) && BOL_DE (0, 7, 2) && Zotero Metadata Importer (1, 0, 33) && Find Duplicates (1, 6, 2) && Clipboard Search (1, 3, 1) && View Manager (1, 3, 2) && Amazon.com secondary source (1, 0, 0) && Kindle Collections (1, 7, 17) && Amazon.com terciary source (1, 0, 0) && Library Codes (1, 0, 27) && Reading List (1, 6, 6) && Read MP3 AudioBook metadata (1, 0, 79) && Goodreads (1, 1, 11) && Job Spy (1, 0, 53) && Annotations (1, 4, 7) && Consolidate All Library Metadata (2, 0, 23)
Traceback (most recent call last):
File "calibre_plugins.consolidate_all_library_metadata. calm_dialog", line 4568, in delete_entire_calm_directory
AttributeError: 'CALMTargetTab' object has no attribute 'target_db_full_path'