Select 'Normal' for Run BSP, and select 'No' for both Run VIS and Run RAD (also be sure to check the 'Don't run the game after compiling' box). Save and compile the BSP by pressing F9 or going to File -> Run Map.

1b, the room is sealed and will be compiled correctly. If you compile this map with that leak, vvis (the portion of the compile that determines visibility data) won't be able to determine the boundaries of the map, since the visleaves will just 'leak' out into the black void outside our map. Also, water won't render correctly if there are any leaks in the map. Worse yet, any area portals, hint brushes and occluders in the map will not work, making them useless. If there are ANY leaks in the map, the compiler won't be able to determine the boundaries of the map, and will attempt to render everything within the map all at once.