Hmm, so not the 3:2 pulldown, at a guess do you mean the whole screen shaking very very slightly? probably when they captured the actual film they did it in realtime instead of using todays individual frame capturing/cleaning methods so the image didn't stay 100% in place going through the projector. (finding it hard to get across my theory, which is probably wrong)

BTW I'm using a Canopus ADVC-100 which has the same analogue-to-digital hardware, I find I have to shift the chroma 3 pixels to the left to get it so the picture doesn't look like the colour is bleeding (use Flaxen's VHS filter, Chroma Shifting I & Q, Horizontal 3 Neg), also to compensate for the lower chroma compression use VirtualDub's internal filter Chroma Smoother in 4:1:1 NTSC DV mode.

edit: if you need to use filters that don't have an interlace button/option, use the internal deinterlace in "Unfold fields side-by-side" before the filter(s) and then afterwards use deinterlace in "Fold side-by-side fields together" mode.

edit2: Just remembered, if you encode the video to mpeg2 with in the wrong field order then any interlacing will stick out like a sore thumb, I have a Sigma Hollywood+ hardware mpeg decoder card in my PC which is extremely useful for checking encoded mpeg files and whole DVDs on a real tv before burning anything to disc, my 2nd one only cost me £9 from eBay including postage (I have one in each machine)