You extracted the patch to the wrong directory.
- create a new temporary folder. Extract the patch to this folder.
- locate the newly created folder called Armageddon 1.3 beta 2 - 24.04.2009 - PHVR and rename it to either Doomsday (if your game is installed in a Doomsday folder) or Armageddon. (if installed in Armageddon folder)
- copy the files from the newly renamed folder so that it overwrites your existing game. You must overwrite the existing files or it won't work. If you don't get the message about overwriting files cancel the copy and try again.