I had this problem the first time I did a "successful" level transition. I don't know what causes it, but it might be the placement of the info_landmark. When I made the map, the landmark came after the transition brush, but I think it's supposed to be before it. Also, having an info_player_start in the new map is a good idea when testing the maps if you're making a mod or something, because you may want to test it from that map, and it's annoying to play the entire mod first. That's a mistake I made with my OpFor map pack.
BTW, another thing that can cause the problem is the naming of the landmarks and level transitions. Make sure it is lowercase, make sure it isn't a long name, and make sure it doesn't have any punctuation in it.