I ran into the same thing. (Same civ, same new name even!) Probably the best workaround will be to devise a city name list you like and work it into the XML so it always comes up that way.
(Though even then I sometimes like to rename stuff ... oh well.)
I don't know if this qualifies as a "bug" because it may have been intentional. There have been times in Civ2, for example, where I changed the city name as I was founding it and then, for my next city, I forgot what the game suggested and wished it would re-suggest it.
But IMO it's far more common for those of us who occasionally rename cities to want to just proceed through the name list.