Hello,
I don’t know if it will help but I worked on websites with the same configuration of yours and I noticed that permalinks were recorded into the database as a post_meta linked to a post ID. The thing is that Custom permalinks records twice the same information : one for the post Id, one for the last post revision ID. So, try to disable post revision feature may help you solve the problem.
Put this line in your wp-config.php :
define(‘WP_POST_REVISIONS’, false);
Bye
