2012 Rulebook p. 5:

"STEP 2: CHOOSE MAP AND STARTING AREAS
The first player chooses the map where the game will occur. After the first player chooses the map, the player to his or her left chooses the starting area—an area of squares inside a purple boundary line—where he or she will set up his or her force. If there are more than two players, continue clockwise around the table until everyone has chosen a different starting area. In two-player games, the chosen starting areas must always be on opposite sides of the map. If either player’s force will not fit within the purple lines, all starting areas increase by one row and one column but cannot overlap another player’s starting area."

So, X and Y are playing a match where the map is pre-determined, such as an IG event.

X wins the roll for first player. Who chooses what side to start on?

I've done it as: if you win roll for player 1, since it's a locked map you don't get that choice and player 2 gets their pick of side.

But since the winner of the roll gets the choice of being player 1 or 2, with a locked map they can chose to be player 2 to get their choice of side.

I don't know the 'official' rule, but I suspect it will be something along the lines of 'check with your judge'. LOL

No, there is no 'check with your judge' (well, at least no more than there is with any ruling). It is exactly like you said.

First player picks map, even when map is picked for him/her by an event description. Second player picks side. If the player that won the roll off wants to pick sides, then he can choose to be second player if he wishes, but then he is stuck being second player (not necessarily a bad thing).