It's happening to me too, here is my script

// Requires HotkeyNet build 147 or higher.
//
// For more info, go to link
//================================================== ==============

//-----------------------------------------------------------
// 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 "D:\Diablo 3\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.
//-----------------------------------------------------------
<Hotkey ScrollLockOn A-Z, 0-9, Numpad0-Numpad9, Tab, Esc, LShift, Space, Plus, Minus, F1-F12 except W, A, S, D; ScrollLockOn Shift A-Z; ScrollLockOn Shift 0-9>
<SendLabel w1, w2>
<Key %Trigger%>

//-----------------------------------------------------------
// DEFINE MOVEMENT KEYS THAT WILL GET SENT TO BOTH WOW'S.
// ADD MORE KEYS IF YOU WANT.
//-----------------------------------------------------------
<MovementHotkey ScrollLockOn W, A, S, D>
<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 Oem5>

<Hotkey ScrollLockOn Oem5 LButton, MButton, RButton, Button4, Button5>
<SendLabel w1, w2>
<ClickMouse %TriggerMainKey%>
<RestoreMousePos>