I've experienced this issue with my bot script. First, I have this, there are a few checks, as I'm using pixelsearch I need to make sure the screen resolution is the correct dimensions for it to be accurate... but really I'm setting the active_id

checkWindow(byref active_id){
width := 816
height := 639
WinGet id, ID, Toontown Rewritten [BETA]
active_id := id
IfWinExist, Toontown Rewritten [BETA]
    {
        WinActivate ; use the window found above
        WinGetPos,winX,winY,curWidth,curHeight
        if(curWidth != width || curHeight != height)
            WinMove, Toontown Rewritten [BETA], , ,  , width, height
        return true
    }
    else{
        TrayTip TTR Tools, "Toontown Application not open", 1, 1
        guiText("txt", "Toontown not open")
        exitGardening()
        return false
    }
}

Then, for controlclick, I do this:

safeClick(x,y){
    checkWindow(active_id)
    MouseGetPos, mouseX, mouseY
    if((mouseX >= 0 && mouseX <= 816) && (mouseY >= 0 && mouseY <= 639))
    MouseMove, x, y
    sleep,25
    ControlClick,X%x% Y%y%,ahk_id %active_id%,,,1, NA
    ControlSend,, {Ctrl},ahk_id %active_id%
}    

and controlsend

checkWindow(active_id)
ControlSend,, {Left DOWN},ahk_id %active_id%
Sleep 1337
ControlSend,, {Left UP},ahk_id %active_id%