I've tested this problem on two PC's running KDE4 until now and got the same problem. It seems autosu-gtk freezes on KDE4, or at least it sits there waiting for a reply while no window or anyting shows up.
I know this sounds silly, but it seems to be like this, anyway.
For example, when I run:
/tmp/autopackage/libexec$ ./autosu-gtk id
it never returns.
I've attached the output of:
/tmp/autopackage/libexec$ strace ./autosu-gtk id >strace_out 2>&1
(ctrl+C'ing after about twenty seconds.)
Something really odd, too, is that when I run autosu-gtk as root, the same happens. You'd say it doesn't have to show a window then, but you guys know the implementation details a *lot* better than I do.
I'm setting priority to High and severity to Critical, since this makes Autopackage unusable on KDE 4 systems.