Alright so this solution works for me... I was able to close 2 windows here. Also I will be able to handle popups based on their name which is cool. It always runs in the background after I have lauched the script. When I want it to end I simply close autoit from task manager or from the task bar area on the right.

While True
If WinWait( Name of your Popup ,   , 1) == 1 Then
    ;Wait for page to load if found
    Sleep(10000)
    ;Close Page
    Send( !{F4} ) 
    Sleep(5000)
    ;Confirm Dialog
    Send( {ENTER} ) 
    Sleep(1000)
    ;Close Lanucher Page
    Send( !{F4} ) 
    Sleep(5000)
    ;Confirm Dialog
    Send( {ENTER} ) 
EndIf
;Let another thread have a turn
sleep(3)
WEnd

Also this is possible from directly within python, details: http://www.parrisstudios.com/?p=308, but you still need autoit3.

If you are having issues with alert boxes you might want to disable them programmatically or create a separate mode in your code that would turn them off based on a condition (i.e. debug mode).

Macro recording programs don t work as well as you might think. Typically macro-recording programs record locations of mouse clicks and timing of key presses. The better macro-recording programs use (typically image processing) and (rarely) computer vision techniques. The solutions that use these techniques are typically VERY EXPENSIVE. (5k-10k per seat) [I can t remember one of the names of the better versions Might be QuickTest, but it was made by a company that was bought out by HP]

I was trying to interact with a webpage with autoit and the stupid javascript alerts kept breaking everything and I finally figured out how to disable them so I thought I would post it here:

#include <ie.au3>

$oIE = _IEAttach( https://www.site.com , URL )

$EventObject=ObjEvent($oIE.document,"IEEvent_")
Func IEEvent_onreadystatechange()
    $readystate=$oIE.document.readystate
    ConsoleWrite ($readystate & @CRLF )
    if $readystate= interactive  then killalert()
EndFunc

while 1
    sleep(100)
WEnd

func killalert()
Local $o_head = $oIE.document.all.tags("HEAD").Item(0)
Local $o_script = $oIE.document.createElement("script")
With $o_script
    .language = "jscript"
    .type = "text/javascript"
    .text =  function alert(message) {}; 
EndWith
$o_head.appendChild($o_script)
EndFunc

Basically what this does is have a function get called in autoit when the page ready status= interactive (apparently this is after most of the page has loaded but before it "runs" anything i think) that inserts some javascript into the page to redefine the alert() function so that it does nothing (no alert dialog to worry about having to click ok on). I have tested this and it works.

If you have the alert() function being called from a frame inside the page then you will have to use the onreadystatechange event and the readystate property of the frame instead of the main document.