there's no real answers in my opinion to questions like that, because
we aren't aware if the whole movie was made in NTSC or if you accidentally made some in those settings and some in PAL, (because when you cross them all sorts of things like that happen) even though you essentially are converting it all to one or the other, the program doesn't like it and sends it all over the shop.
it could also be that when your burning it your got the writing speed on to high, i always turn it down to it's lowest so as not to miss frames, get jumping footage etc etc.
i have burnt the same movie over and over and got a different result every single time from how fast the burner writes, so try slowing it down so not to miss any files etc whatsoever.
other than that, who knows with this sort of problem
could be your program, could be missing files, corruption etc etc