> It made sense to simply
> cut/paste the clips into a new sequence with the
> proper settings, but the results were not as
> expected.
Do you mean SD NTSC? That would result in a difference in frame sizes as HD has more lines than SD. I was once trying to output HD on SD, and i realized that it didn't recompress the aspect ratio when i copied and pasted the clips, but it worked when i nested the sequence.
Is there also a sync issue? Try thrashing render files before copying, as rendering would force convert the 23.98 frame rate to 29.97 fps.