srcds_run is broken (sorta) – A new orangebox folder is created when you start your game (UPDATE: FIXED)
Have you tried to install the new Counter-Strike: Source game server update and all the sudden an entirely new oragebox folder was created and a new copy of the game was downloaded to it?
Yeah, its a bug, its not you. Valve has once again released confusingly undocumented and broken stuff to us.
To fix it, edit line 296 of srcds_run and change DEPOT_ROOT=”.” to DEPOT_ROOT=”..”
That will source the update from the directory above and everything will work fine!
Update: Steam has fixed this error!