Steam – Zbots not working with Counter-Strike 1.6 steam version

What you're looking for is called remote-console, or rcon. It's built right into the game; to use it, set rcon_password to the same value on the server (in server.cfg) and client (in the console), then type into the client-console rcon <command> for any commands you want to run on the server.

You can use rcon outside of the game, too. The most popular tool for this is HLSW.

Presumably your copy has some method of circumventing Steamworks that persists even when you attempt to download changed files from Steam. Backup your saves (located in "C:\Users\Your Username\Documents\My Games\Borderlands\SaveData" for Windows 7/Vista and somewhere similar for XP) and remove Borderlands entirely. Ignore step one and step three, simply let Steam install the game. This should restore full Steam compatibility.