The agent fixed them again, told me to keep an eye on them. Also suggested that I call AF and get seats assigned. Said that she thought that once one of their agents had touched them to do that, they might stick. I'll try anything at this point!
I called AF, they made the assignments. I've also now printed out the confirmation page from the AF site with the AF locator, just in case things go wrong again.
The last thing I want is for this to happen again closer to the time and for us to lose the flights.