I've substituted the code you gave me, but perhaps in the wrong place? I'm still having the same problem. And I have indeed unchecked the option you suggested. Here's the script I'm running, in its entirety.

Code:
//================================================================
// SAMPLE SCRIPT FOR TWO WOW'S ON ONE PC 
//
// Instructions: Copy this entire script (all the blue writing
// on gray background including comments). Save it in a file. 
// Load it into HotkeyNet.
//
// Toggle the scroll lock key to turn hotkeys off and on. (You 
// can change this if you want, just like you can change 
// everything else with HotkeyNet.) 
//
// Requires HotkeyNet build 147 or higher.
// 
// For more info, go to www.hotkeynet.com 
//================================================================

//-----------------------------------------------------------
// PRESS CTRL R TO RENAME WOW'S IF YOU LAUNCH THEM MANUALLY 
//-----------------------------------------------------------
<Hotkey ScrollLockOn Ctrl R>
    <SendPC local>
        <RenameWin "World of Warcraft" WoW1> 
        <RenameWin "World of Warcraft" WoW2> 

//-----------------------------------------------------------
// SUBROUTINE TO LAUNCH AND RENAME A COPY OF WOW.
//-----------------------------------------------------------
<Command LaunchAndRename>
   <SendPC %1%> 
      <Run "c:\users\ravyn\desktop\World of Warcraft\WoW.exe">
        <RenameTargetWin %2%>

//-----------------------------------------------------------
// HOTKEY TO LAUNCH AND RENAME BOTH WOW'S.
//-----------------------------------------------------------
<Hotkey ScrollLockOn Alt Ctrl L>
    <LaunchAndRename Local WoW1>
    <LaunchAndRename Local WoW2>

//-----------------------------------------------------------
// DEFINE MAIL LABELS FOR SENDING KEY STROKES 
//-----------------------------------------------------------
<Label w1 Local SendWinM WoW1>
<Label w2 Local SendWinM WoW2>

//-----------------------------------------------------------
// DEFINE HOTKEYS FOR ALL KEY COMBINATIONS THAT WILL GET
// SENT TO BOTH WOWS. ADD MORE KEY COMBO'S IF YOU WANT. 
//-----------------------------------------------------------
<KeyList WoW 0-9, Numpad0-Numpad9, Divide, Multiply, NumpadMinus, Tab, NumpadPlus, Backspace, Insert, Home, PgUp, PgDn, Delete, F1-F12, Esc, Oem1-Oem7, except OEM2, w, a, s, d, q, e, x>
<Keylist All 0-9, A-Z, Space, Esc, Enter, Tab, Oem1-Oem7>

<Hotkey ScrollLockOff MyList; CapsLockoff Shift MyList; CapsLockOff Alt MyList; CapsLockOff Ctrl MyList>
	  	 <SendLabel w1, w2, w3, w4, w5>
   	<Key %Trigger%>
<Hotkey ScrollLockOn All>
	  	 <SendLabel w1, w2, w3, w4, w5>
   	<Key %Trigger%>
//-----------------------------------------------------------
// DEFINE MOVEMENT KEYS THAT WILL GET SENT TO BOTH WOW'S.
// ADD MORE KEYS IF YOU WANT. 
//-----------------------------------------------------------
<MovementHotkey ScrollLockOn up, down, left, right>
<SendLabel w1, w2>
<Key %Trigger%> 

//-----------------------------------------------------------
// BROADCAST MOUSE CLICKS. HOLD DOWN OEM3 (ON U.S. KEYBOARDS,
// THAT'S THE SQUIGGLE KEY IN UPPPER LEFT CORNER) WHEN YOU 
// WANT TO BROADCAST.
//-----------------------------------------------------------
<UseKeyAsModifier Oem3>

<Hotkey ScrollLockOn Oem3 LButton, MButton, RButton, Button4, Button5>
   <SendLabel w1, w2> 
      <ClickMouse %TriggerMainKey%>]