Then don't try to set cl_consolehistory in your binds script.
It's probably autogen.cfg that he's execcing, or he copied his autogen into his autoexec.
The way I solved this problem is by making a separate folder for my binds. I called this folder 'binds', and it's in my base folder. Files and folders in the base folder can also be used when playing on servers with separate fs_games, but they don't have priority.
So, /exec binds/default.cfg, and whoopee, I get all my binds. Then, I can set mod specific settings using the console, and they'll be saved in that fs_game's autogen.