Looks like i got it, had to change w1 w2 w3 in IF statements to WoW1 WoW2 WoW3. Was checking an invalid varible.

Code:
//-----------------------------------------------------------
// FTL target & follow
//-----------------------------------------------------------
<Hotkey ScrollLockOn 1, 0>
       <Passthrough>
       <If ActiveWinIs WoW1>
          <SendLabel w2, w3>
             <Key RCtrl RAlt RShift %Trigger%>
       <Else If ActiveWinIs WoW2>
          <SendLabel w1, w3>
             <Key RAlt RCtrl %Trigger%>
       <Else If ActiveWinIs WoW3>
          <SendLabel w1, w2>
             <Key RCtrl %Trigger%>
       <Endif>