Do your key strokes record in the top wow that way? I have my script set like this to send to both wows.

~1::
KeyWait 1
IfWinActive, World of Warcraft
{
ControlSend,, 1, ahk_id %wowid1%
ControlSend,, 1, ahk_id %wowid2%
Return
}
~2::
KeyWait 2
IfWinActive, World of Warcraft
{
ControlSend,, 2, ahk_id %wowid1%
ControlSend,, 2, ahk_id %wowid2%
Return