Such a problem, I just can not find an approach to clicking the Save or Save as button in the pop-up IE11 window. I use Java + AutoItX, but either the hands are crooked, or the head is bad, nothing happens. 
To transfer simply pressing buttons of the type {ENTER} or {TAB} is not an option at all. Maybe there are other tools that can work with windows DirectUIHWND or IEFrame. I can get the Title window, get HAndle too, but how to get the list of buttons or press a specific button does not work.