Are you viewing the footage on a computer monitor or broadcast reference monitor?
Your computer display (and your LCD, plasma, LED TV) is a progressive scan monitor. So when you preview interlaced footage on there you tend to see the scan lines (odd and even). If you pause it then it's really pronounced. But even when it plays you'll see the interlacing in any motion areas (running, cars driving by, hand waving, etc.).
Preview your footage on an interlaced monitor and you shouldn't have any problems. If your final delivery is intended for progressive displays (projectors, YouTube, Vimeo, etc.) then you'll need to de-interlace your material before final delivery.
Ryan Holmes
http://www.ryanholmes.me
vimeo.com/ryanholmes
