The INI format continuation mechanism is to leave a space at the beginning of lines that should be included in the previous line--which includes *all* of the lines for custom_columns_settings.
Your custom_columns_settings, at least, need leading spaces on all the continuation lines. You didn't use [code] tag, so we can't see what leading white spaces you already have.
Like so:
Spoiler:
Code:
[defaults]
is_adult:true
[epub]
include_images:true
jpg_quality: 100
keep_summary_html:true
make_firstimage_cover:true
[archiveofourown.org]
use_basic_cache:true
username:XXXXXXXX
password:XXXXXXXX
always_login:true
is_adult:true
extra_valid_entries:fandoms, freeformtags, freefromtags, ao3categories, comments, chapterslashtotal, chapterstotal, kudos, hits, bookmarks, collections, byline, bookmarked, bookmarktags, bookmarksummary, bookmarkprivate, bookmarkrec, restricted, series00, series00Url, series00HTML
fandoms_label:Fandoms
freeformtags_label:Freeform Tags
freefromtags_label:Freeform Tags
ao3categories_label:AO3 Categories
comments_label:Comments
chapterslashtotal_label:Chapters/Total Chapters
chapterstotal_label:Total Chapters
kudos_label:Kudos
hits_label:Hits
collections_label:Collections
bookmarks_label:Bookmarks
bookmarked_label:I Bookmarked Story
restricted_label:Restricted to Registered Users
series00HTML_label:Series
make_linkhtml_entries:series00,series01,series02,s eries03
replace_metadata:
chapterstotal=>[0-9]*[^0-9]+[0-9]*=>
custom_columns_settings:
characters=>#characters
ships=>#relationships
rating=>#maturityrating
warnings=>#warnings
numChapters=>#currentchapters
numWords=>#wordcount
status=>#status
datePublished=>#dateposted
dateUpdated=>#dateupdated
fandoms=>#fandom
freeformtags=>#additionaltags
freefromtags=>#additionaltags
ao3categories=>#category
comments=>#comments
chapterslashtotal=>#chapterslashtotal
chapterstotal=>#totalchapters
kudos=>#kudos
hits=>#hits
bookmarks=>#bookmarks
collections=>#collection
restricted=>#restricted
bookmarked=>#bookmarked
bookmarktags=>#bookmarktags
bookmarksummary=>#bookmarksummary
bookmarkprivate=>#bookmarkprivate
bookmarkrec=>#bookmarkrec
series00=>#series1
[overrides]