As you know when you change keyboard layout with alt-shift it affects all the windows of current application. Is it there any program which changes the behavior to per window?
OS: Windows 7
It should be possible with AutoHotkey.
In the "Text Services and Input Languages" screen (where you define the keyboard layouts and set the default one), go to the "Advanced Key Settings" tab. There you can assign a different hotkey per input language (=keyboard layout).
Once you've assigned the hotkeys to the desired languages, an AutoHotkey script could trigger the hotkey when it detects a specific window opens or has the focus (=is activated). The window can be detected by title, class, text in the window, ... or even a mix of two or three.
I don't think that is possible, the changes are global.
But you can setup a VirtualBox and run the application in seamless mode with a different keyboard layout. :)