I may have an answer for you, I had a folder named .playlist (in my Documents folder)
It was empty, so I deleted it. Now Kino2 forgets it's playlist, just like you described.
I have my playlist.m3u saved in my Movie_Files folder.
I just created the .playlist folder again, opened my playlist.m3u, resaved the playlist and closed Kino2.
When I opened Kino2 again, my playlist loaded automatically, like it should.
.playlist is located here on my C3100:
/hdd3/Documents/.playlist
playlist.m3u is located here:
/hdd3/Documents/Movie_Files/playlist.m3u
BTW, I also have ZPlayer installed, but I don't think it effects anything that I described above.
EDIT: I just checked /hdd3/Documents/.playlist (in Tree!Explorer), and it has a copy of playlist.m3u in it now.
(I didn't copy it there, Kino2 must have copied it there).