Okay. The blue texture means that the blue areas are sopossed to be transparent when viewed in-game.
When you compile and run the map, the blue squares will be black.
In order to make them transparent, you have to turn the brush into an entity, make it a func_wall. Render mode: solid Render FX: 255
And you have a brush outside world. This is not necessarily a leak, but there's a brush either too close to the edge of the grid, or off of it completley. you want to have your map as close to the center (X,Y,Z) origin of the grid as possible. Or else errors such as this:
Error: Entity <WHATEVER>, Brush <NUMBER>: outside world
can occur.
When you select things. They turn red. Darker colors tend to turn black. blue turns black. Red turns black, Sometimes even green. It just happens really. (in the texture application tool, you can tick the [hide mask] box to get rid of the highlight [mask] to better see the texture you're manipulating. Unfortunatley, i don't know a way to hide the mask using just the normal select tool)