I'd suggest renaming the windows as they are opened via that subroutine rather than waiting until they are all open. The setup in the default scripts are not ideal, as I explain in the Configuring a HotKeyNet Starter Script guide on my site.

Code:
//----------------------------------------------------------
// 	SUBROUTINES FOR WOW*5
//----------------------------------------------------------
//*
//----------------------------------------------------------
// 	WoW LAUNCH AND RENAME
//----------------------------------------------------------
//*
<Command LaunchAndRename>
<SendPC %1%>
<Run %2%>
<RenameTargetWin %3%>
<RemoveWinFrame>
<wait 500>
<text %4%>
//+

//----------------------------------------------------------
// 	WoW RESIZE AND POSITION
//----------------------------------------------------------
//*
<Command ResizeAndPosition>
	<SendPC Local>
		<SendWinM %1%>
			<SetWinRect 0 0 1920 1050>
				<SetWinRegion none>
		<SendWinM %2%>
			<SetWinRect 1920 0 480 270>
				<SetWinRegion none>
		<SendWinM %3%>
			<SetWinRect 2400 0 480 270>
				<SetWinRegion none>
		<SendWinM %4%>
			<SetWinRect 1920 270 480 270>
				<SetWinRegion none>
		<SendWinM %5%>
			<SetWinRect 2400 270 480 270>
				<SetWinRegion none>
				
//+

//----------------------------------------------------------
// 	WoW *5 LAUNCH HOTKEY 
//----------------------------------------------------------
//*
<Hotkey LCtrl  LAlt w>
	<if WinDoesNotExist WoW1>
		<LaunchAndRename Local "G:\WoW\World of Warcraft\Wow-64.exe" WoW1 PASSWORD>
		<endif>
	<if WinDoesNotExist WoW2>
		<LaunchAndRename Local "G:\WoW - Slave1\World of Warcraft\Wow-64.exe" WoW2 PASSWORD>
		<endif>
	<if WinDoesNotExist WoW3>
		<LaunchAndRename Local "G:\WoW - Slave2\World of Warcraft\Wow-64.exe" WoW3 PASSWORD>
		<endif>
	<if WinDoesNotExist WoW4>
		<LaunchAndRename Local "G:\WoW - Slave3\World of Warcraft\Wow-64.exe" WoW4 PASSWORD>
		<endif>
	<if WinDoesNotExist WoW5>
		<LaunchAndRename Local "G:\WoW - Slave4\World of Warcraft\Wow-64.exe" WoW5 PASSWORD>
		<endif>
<ResizeAndPosition WoW1 WoW2 WoW3 WoW4 WoW5>
Or you can try the version I had to use for EQ2

Code:
//----------------------------------------------------------
// 	SUBROUTINES FOR EQ2*2
//----------------------------------------------------------
//*


//----------------------------------------------------------
// 	 RESIZE AND POSITION
//----------------------------------------------------------
//*
<Command ResizeAndPosition>
	<SendPC Local>
		<SendWin %1%>
			<SetWinRect 0 0 1920 1050>              
		<SendWin %2%>
			<SetWinRect 1920 0 960 540>
//+


//----------------------------------------------------------
// 	EQ2 LAUNCH AND RENAME
//----------------------------------------------------------
//*
<Command LaunchAndRename>
	<SendPC %1%>
		<wait 500>
		<TargetWin "EverQuest II">
			<CloseWin>
				<Wait 500>
	<Run %2%>
		<wait 15000>
	<TargetWin "EverQuest II">
		<ClickMouse Window 750 525>
			<wait 7000>
	<TargetWin "EverQuest II">
		<ClickMouse Window 350 275>
			<text %3%>
				<wait 50>
	<Key Tab>
		<text %4%>
			<wait 50>
	<Key Enter>
		<wait 3000>
	<TargetWin "EverQuest II">
		<ClickMouse Screen 1250 750>
			<wait 5000>
	<RenameFromPath %5% %6%>
		<ResizeAndPosition MAIN SLAVE>
	<wait 500>
		<TargetWin "EverQuest II">
			<CloseWin>
	<Wait 500>
//+



//----------------------------------------------------------
// 	WoW *5 LAUNCH HOTKEY 
//----------------------------------------------------------
//*
<Hotkey LCtrl  LAlt w>
	<if WinDoesNotExist SLAVE>
		<LaunchAndRename Local "G:\EQ2 Slave\EverQuest2.exe" ACCOUNT PASSWORD "G:\EQ2 Slave\EverQuest2.exe" SLAVE>
		<endif>
	<if WinDoesNotExist MAIN>
		<LaunchAndRename Local "G:\EQ2\EverQuest2.exe" ACCOUNT PASSWORD G:\EQ2\EverQuest2.exe MAIN>
		<endif>
<ResizeAndPosition MAIN SLAVE>