I have also face this problem too, but after plugin update I generally visit the permalink option page and save the setting once and visit any page/post with custom link and also update the page. After which every things seems to working again…
Can you share what you did to rectify it?
thanks.
Same problem.
I save posts as drafts and then edit contents/permalinks. After that published posts show 404. Disabling Permalink Editor magically solved the problem.
I was using 0.2.7 successfully, and updated to 0.2.10 and my custom links stopped working. Reverted and they are working again.