There's nothing that I know of where JKR has specified that or anything... I think it could probably be argued either way to some extent. My own impression was that he was going in to his second year only because Ginny tells Albus that "we wrote to James three times a week last year", which always seemed to imply to me that the previous year had been James' first year (as it was said in relation to Albus' first year). If it's important to you to make him a third-year, though, I don't think anyone'd squawk tooooo loudly ;-) My 2 Knuts is to just put an A/N somewhere that explains it, if you really want it to go a particular direction.