I dunno if this may help or not, but say you start a game of Civ2 and you build a couple cities (assume Celts and you built Cardiff & Kells), but dont like the way things are going and restart. well, if you play the same civ without closing the game out first, the game will not use the old cities name, it will continue with the cycle and use Carmarthen as your initial city - it will do this UNLESS you close the game window entirely and start again.
Maybe in your scenario building you did a few restarts and lost those early city names?