The update didn't help with the cheats at all
I like the ability to edit them straight in the app though, so that is good.
Here is what the automatic cheat download gives for Final Fantasy 9 North American versio http://i.imgur.com/9vzku.png
Here is my own cheats http://i.imgur.com/dv93x.png
and this is what it shows after http://i.imgur.com/IUlAm.png
Even that one cheat doesn't work at all. After that I tried to find different cheats from the Internet. None of the cheats I tested worked. I even tried to uninstall FPSe, removed cheat files and re-installed it. No help.
Those both cheats worked perfectly prior the few previous updates so those ones aren't incorrect.
edit: most of the cheats worked on Final Fantasy 7 though. So might it be that the problems now are just with FF9? Though, not all cheats were displayed with the FF7 either.