I had done some mapping in both CS and regular half-life but for some reason I'm running into trouble with the grates, ladders, and other textures that have portions that are supposed to be transparent. When I compile the map and run it, the transparent sections are just as opaque as the rest of the texture...

Any ideas?

render mode = solid
FX amount = 255
that will give you transperency
(it has to be an entity)

Sorry, I probably wasn't clear enough. I'm talking about objects that have PORTIONS that are supposed to be transparent (like ladders).

The rung portion of the ladder is yellow while the portion between the rungs should be clear (as if it wasn't there), when I compile and test the map this space shows up black...

As he said, you will need to make it have render mode Solid and FX amount 255.

make sure your texture has "{" in front of it liked for example "{ladder". all textures with "{" in front of it will have blue parts which are invisible ingame.

just turn the brush with this texture into and entity and set is properties as error 404 name not found and ShdwStal posted.