We saw this bug and thought we had it fixed. One thing that affected this bug's behavior in our sleuthing was whether or not the game started up in windowed mode.
Please try this - right click the "Portal" title in the Steam game list, and select Properties. In that dialog click the "Set Launch Options" button. Then in that text field just put this text:
-windowed
This will cause the game to start up in windowed mode (which you can then change back to FS using Options->Video tab)
This is just an experiment for you to try, to let us know if you see the same behavior that we did. It's a very strange bug. It's not portal depth related, it's a rendering bug.