Indeed there is a bug with the update of the thumbnail.
The good news is that I found exactly where and why, and it is very easy to fix.
The bug exists since several months, but the bright side is that I can easily find all those which were not updated: the new thumbnail is still laying around. I just have to write a small script that will replace the forgotten thumbnails, by checking if the pic wasn't updated again by an admin in the meantime (otherwise it will just delete the useless new thumbnail).
I'll already fix today the code for future picture replacements, and for the previous ones I'll try to write a script to clean that in the next days.