So you are saying that in the folder "main" you have all iwd's + all localized files from 1.3?
And then in the fs_game you have the same mod for all 3 versions?

If you also use that "main" both for 1.2 and 1.3 servers, the players from 1.2 have to download a big-ass iw_15.iwd because it's not the same on the client