DV to mpeg2 certain sections have jerky playback.

[funkyGOK]

I am experiencing problems when I try to encode a 17 minute DV quicktime file to PAL mpeg2 4Mb/s about 90% of the film is encoded correctly though there are certain sections that display jerky playback.
I am using a G3 B/W 400MHz and it takes about 12/13h.
If I make a small film file of the jerky section say 1 1/2 minutes
and encode it, it plays back perfectly.
Any ideas how I could solve this problem?

[Tommyknocker]

First, try to change the field frame order. Then try a different brand of media.