Not sure. But since I'm using mine for back up, I don't care. I'm not breeding on it except to make fodder for trading to my other game, because it's cheaper than catching. I'll have to get a White ROM file up to the point of trading and see if the union room problem happens with it as well.
As a note, you could use the wrong ROM to run it solely while trading, and then rename it the correct name so it's generating pokes correctly via the correct ROM.