Ok, so if you send the A window to the bottom, then the top most window is not currently the focus, so maybe send a WinActivate to that window. Probably means you'd need to track the stack positions yourself so you knew what order the windows should be in, as I can't spot a GetTop or anything useful like that (less of a problem with 2, more a problem with 3+).

If you were attempting to get around the Click Rightclick thing which might target something, does a Keypress work for the focus? A good keypress to send would be F1 (usually set to Target Self in default setup). This may not work at all as the WinSet may not be changing the focus input. If you do need the mouse, then I'd be inclined to save the current mouse position, do some math and get it to leftclick the mouse on the titlebar/border of the window where it is not likely to have any impact, and then put the cursor back where it was.

Another option might be to wrap the WinActivate with some keydown/ups. A bit of a read through the comments in the code suggest if you did a KeyDown ALT, followed by your WinActivate, then a KeyUp ALT, it might all work out (because hitting the ALT key in Windows does some behind the scenes stuff getting it prepped for window swapping!)