Below is my AutoIt script (UI3_Authentication.au3) for handling a Windows authentication pop up.
AutoItSetOption(\"WinTitleMatchMode\",\"2\")
WinWait(\"Aut
I faced the same problem. AutoIt works well with selenium if it is running in an "open" desktop. If I use a Virtual Machine with a open session(seeing what is happening), even minimized, it works fine, but if I close the remote desktop(session ends), AutoIt script shows success but do nothing.
The "solution" was to keep virtual machine "open" by connecting it with TightVNC. Even closing the window, the VNC keeps the logon alive and AutoIt works without problems.
Hope this info helps you. Its not a solution but maybe you can workaround it.