opened HKN, loaded it, Opened both copies of WoW, and nothing happend. I even closed it out and opened HKN and loaded the script while both copies of WoW were open.
Are you actually running the hotkeys as listed in the script? HKN doesn't just take over your WoWs, you have to tell it what to do with the proper hotkeys:

]PRESS CTRL R TO RENAME WOW'S IF YOU LAUNCH THEM MANUALLY
//-----------------------------------------------------------
<Hotkey ScrollLockOn Ctrl R>
HOTKEY TO LAUNCH AND RENAME BOTH WOW'S.
//-----------------------------------------------------------
<Hotkey ScrollLockOn Alt Ctrl L>