Comment 9 for bug 1008113

Ok, I think this has something to do with the bunch of invisible windows, that FF has open.

If you try this with FF, you can see this:

ff = App("firefox")
for i in range(100):
    w = ff.window(i)
    if not w: break
    print w

So before running the snippet, manually make a "real" FF window the frontmost, and I think it should work.
I have always tested this way and it worked for me, even if the FF window was somewhere behind other windows.

When I am right, then there is currently no solution for that, because it is not possible, to get a special window to the front by saying:
ff.window(4).focus()

@Benny
please paste here, how you did your "switch between Notepad and VLC Media Player"