I am Having this issue in The Portal 2 Authoring Tools, when I Run the map, some brushes end up black.
I cannot figure out what the issue is, as I am semi-new to Hammer. Here are some Screenshots Of my Problem.

Fullbright: http://i.imgur.com/u6PSj.jpg

Regular Lighting: http://i.imgur.com/9Sx5c.jpg

That is a problem with the model you are using in the wall. Inside your model find the value that says 'disable shadows' and set it to yes.

The problem will also disappear when you compile in Full mode.