Did you ever figure this out? I have the same exact issue. Achievements work fine on everything else I've tried, but PS1 and N64 will not work. If I go to the retroarch menu, achievements are disabled. I re-enable them, save the configuration multiple times, but as soon as I reload any N64 or PS1 game, it gets disabled again.
I've even manually edited the system\configs\retroarch\retroarch.cfg file and it reverts back as soon as I load an n64 or ps1 game.