I have just tried to use the Cordon tool, but the part of my map that i want to look at, no brushes are showing. All the props are there, just no brushes.

Go to the visgroups bar and make sure everything is checked/visible.

Everything is checked but the its still only the props that are visible.

Are you sure that the cordon extends over the whole part of your map in all 3 grids? (not just the top view)
When you create a new cordon it will be 0 width on other other grids from where you drew the cordon on.

Here are 2 photos, 1 in hammer, the other ingame

http://imageshack.us/photo/my-images/155/cordon.jpg/
http://imageshack.us/photo/my-images/851/cordon01.jpg/

I can see that the door is covered by something at the left side.
Like all brushes would be nodraw, but they aren't.
What about not using Cordon for compiling or build closed rooms and cordon around them?

Personally I don't see anything wrong with what you have to make it look like that (other than only compiling entities).
But I've found cordon to be extremely buggy in the Portal 2 hammer. Whenever I compile it says something similar to "overflow small heap block" and takes about 4x as long to compile. Unfortunately cordon is a really useful tool that I use to check out lighting without a massively long compile time (well 4 minutes is long just to see a bit of lighting ).

You could always manually mimic cordon like Skotty said by using VisGroups and sealing it with a large box.

Thanks guys, i thought it was the cordon being buggy and not what i have done, will give it a go by sealing it off without the cordon.