Good morning.
Yes i have tried that... i have played the resulting video file in VLC, Dragonplayer, Mplayer and Xine and in all of them it was precisely the same, i.e. stretched to fill the 4:3 aspect. The black bars simply were not there.
I then uploaded a smaller file created the same way (just a couple of minutes of the same movie) to three of my phones (Samsung L700, U800 and F309) and it was the same there, i.e. stretched to fit 4:3.
Which is how i came to the conclusion that ffmpeg respectively it's WinFF front-end simply "don't know" how to handle the black bars automatically in the way that "Super" did under Windows. Sadly i do not have any Windows machine available for testing as i succeeded pretty much to convert my entire environment including office and colleagues to Linux

And "Super", while installing fine, does not run under Wine/Linux.......
For now i am fine with doing the black bars manually via the "padtop/padbottom" commands however having this done automatically would be way better as movies tend to come in all sorts of formats/aspect ratios these days......
Kind regards.....
Thanh