Even if they had announched here that this was fixed, I can say it was not fixed.
And thats why you are also having this problem.
No matter how helpful the WP Toolkit is, I have uninstalled it, and since then all my websites and permalinks are working fine like before.
I would advise you to do...
My only solution for the time was to uninstal wpToolkit, and deactivate the pretty URL's on my affected websites, and everything is working.
And ofcourse now I need to spend more time to re-enable and fix the permalinks to be pretty once more.
I still have this problem today and this is causing me huge problems with many custom websites.
I got the latest version 4.8.2-3642 and my websites who have custom links are still broken and returning a 404 error.