Ibn Ezra in his long commentary to Shemot 1:11 and 12:37 claims they are different places and that the Jews lived in Ra'meses and not in Ra'amses which they built. (According to this it would be a correctable mistake when reading the Torah since it totally changes the meaning.)
Chizkuni to Shemot 12:37 assumes they are the same place when he says they gathered in Ra'meses which is where they worked.
R. Saadya Gaon translates both as עין שמס (like שמש = sun) but that's not a strong proof since both names clearly derive from the Egyptian sun god Ra whether or not they are the same place.
Most commentaries don't note the difference and it's hard to tell if that means it was obvious to them that they refer to different places or if it was obvious to them that they refer to same place.