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>
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