I'm afraid "Remember last movie position" does something different from what you expect of it:
http://forum.bsplayer.org/viewtopic.php?p=22458#22458
I think you need to select "Remember movie window size" under Options > Preferences > Video
and (if checked) to
unselect "Don't remember movie window position" (also under video preferences).
Further (re saving of config/preferences):
http://forum.bsplayer.org/viewtopic.php?p=21159#21159