@thelostsoul I just looked up which emulators are supported and the most common Mega Drive emulators does. So, thats not the problem here I guess. https://docs.libretro.com/guides/retroachievements/
I enabled RetroAchievements 2 weeks ago too on my Pi3 and not all systems did work, when they should. I can't say why. Maybe this have something to do with the RetroAchievement site itself? So, try again later. Here are the systems I tried to enable by changing the configuration files. I need to retest them too.
Working cheevos: nes, snes, gb, gbc, gba, md, ms, gg
Not working cheevos: ngpc, a2600, pce
Maybe add the information from this thread first: https://retropie.org.uk/forum/topic/3/read-this-first