Ok, what's going on is not that anything is minimizing, it's that the hole you are punching in the big window is using the wrong position. The second window is just hidden behind the main window.
Code:
<TargetWin %1%>
<SetWinRegion 1990 0 600 500>
This code is telling HotKeyNet where to put a hole in the main window. The hole is what allows you to see the second window through the large window. You have it starting at 1990 pixels into the window. Since you're using TargetWin, you can't use screen position to establish the hole. This code is actually putting the hole you need somewhere on the upper left corner of screen 3. Change it to 0 to have the region start over WoW2 where it belongs.
Also you need to clear the previous region when you swap windows otherwise the windows will keep resizing with huge chunks missing from them. Finally, I added a RemoveWinFrame to the LaunchAndRename to get rid of the window borders.
Code:
//-----------------------------------------------------------
// 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:\Program Files (x86)\World of Warcraft\WoW.exe">
<RenameTargetWin %2%>
<RemoveWinFrame>
//-----------------------------------------------------------
// 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, Plus, Minus, except W, A, S, D, Q, E>
<SendLabel w1, w2>
<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%>
//----------------------------------------------------------------
// RENAME WINDOWS AND REMOVE BORDERS
//----------------------------------------------------------------
<Hotkey Ctrl R>
<RenameWin World WoW1>
<RemoveWinFrame>
<RenameWin World WoW2>
<RemoveWinFrame>
//----------------------------------------------------------------
// SET PIP CONFIGURATION
// Usage: <SetPip BigWindowName LittleWindowName>
// This command is called by <Hotkey F1> which is defined below.
//----------------------------------------------------------------
<Command SetPip>
<TargetWin %2%>
<SetWinSize 600 500>
<SetWinPos 1990 0>
<TargetWin %1%>
<SetWinPos 1990 0>
<SetWinSize 1925 1170>
<TargetWin %2%>
<SetForegroundWin>
<SetWinRegion none>
<UpdateWin>
<TargetWin %1%>
<SetWinRegion 0 0 600 500>
<SetForegroundWin>
//----------------------------------------------------------------
// TOGGLE PIP CONFIG WITH HOTKEY
//----------------------------------------------------------------
<Hotkey ScrollLockOn F1>
<Toggle>
<SetPip WoW1 WoW2>
<Toggle>
<SetPip WoW2 WoW1>
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