Silly mistake on my part,
At some point I defined my wp-content directories right in wp-config.
define( 'WP_CONTENT_DIR', '/home/user/public_html/site/subdirectory/wp-content' );
define( 'WP_CONTENT_URL', 'http://www.seocial.ly/site/subdirectory/wp-content' );
Completely overlooked this when editing my wp-config.
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