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I made a basic script to press w on both of my accounts
<Hotkey w>
<PassThrough>
<SendWinSF WoW2>
<Key w>
but I tried running it and if I have wow1 focused then only wow1 moves and if I focus wow2 then neither move, I've tried running as admin and manually renaming my windows and nothing has worked.
You are defining it as a hotkey and not a movement hotkeynet, which means that HKN will not keep the key pressed while you are holding it down. Also if you are focusing WoW2, nothing in your script is setup to send the key to WoW1 so that client will not receive the key.
I'm also a bit uncertain why you'd need passthrough for movement keys as well as all it does is allow the currently focused window to receive the keypress, even if it is not defined to do so by your sendlabels.
The hotkeynet site has documentation for movement keys here: http://www.hotkeynet.com/p/movement.html