Came here to see if anyone else was having a similar issue and if there was a fix for it. I can open wow fine manually but when I use my script I get the same blank grey error box as everyone else. I did manage a work around for this problem but hope someone can come up with a better solution. Anyway, here is what I did:

Open each instance of wow manually
Then use HKN program menu to manually rename each instance. The rename option is under the Actions menu. Right click the title bar of the window you want to rename when the Rename option is open. Then type the windows new name.
Then I just use the hotkey I have set up that Configures the position of the windows.

Note: Depending on how your config file is set you may want to add a <RemoveWinFrame> to your ResizeAndPosition command.

Hope this helps and that we can come up with a better solution soon.

Here is the relevant code for reference:

//----------------------------------------------------------------
// Alternate Window CONFIG WITH HOTKEYS Alt Shift F1-F5
//----------------------------------------------------------------
<Hotkey ScrollLockOn Alt Shift F1>
<ResizeAndPosition 1 2 3 4 5>
<SetActiveWindowTracking On>
<SendWin WoW1>
<Key Oem6> // Key to send to focus win to tell slaves to follow.

<Hotkey ScrollLockOn Alt Shift F2>
<ResizeAndPosition 2 1 3 4 5>
<SetActiveWindowTracking On>
<SendWin WoW2>
<Key Oem6>

<Hotkey ScrollLockOn Alt Shift F3>
<ResizeAndPosition 3 1 2 4 5>
<SetActiveWindowTracking On>
<SendWin WoW3>
<Key Oem6>

<Hotkey ScrollLockOn Alt Shift F4>
<ResizeAndPosition 4 1 2 3 5>
<SetActiveWindowTracking On>
<SendWin WoW4>
<Key Oem6>

<Hotkey ScrollLockOn Alt Shift F5>
<ResizeAndPosition 5 1 2 3 4>
<SetActiveWindowTracking On>
<SendWin WoW5>
<Key Oem6>

//-----------------------------------------------------------
// SUBROUTINE TO Position Windows for 5 boxing.
//-----------------------------------------------------------
<Command ResizeAndPosition>
<SendWinM WoW%1%>
<RemoveWinFrame>
<SetWinRect 0 0 1920 1050>
<SendWinM WoW%2%>
<RemoveWinFrame>
<SetWinRect 1920 0 840 525>
<SendWinM WoW%3%>
<RemoveWinFrame>
<SetWinRect 2760 0 840 525>
<SendWinM WoW%4%>
<RemoveWinFrame>
<SetWinRect 1920 525 840 525>
<SendWinM WoW%5%>
<RemoveWinFrame>
<SetWinRect 2760 525 840 525>