In my experience there isnt a lot you can do about this, it just isnt being compiled exactly right. As a note though, you dont need to apply nodraw to any faces which are on the outside of the map, they are automatically stripped off anyway. The only time you need no draw on brushes in this way is for a face that is not on the outside of the map but can never be seen. Apply the same texture as the top to the sides and see if that changes anything is my suggestion.