Heather, here are some notes for you:
1. the interlacing would appear because you chose to render the motion *that AE created* as fields. If you made the layers move, you’d see interlacing on an interlaced render.
2. If you used all Illustrator sources, and rendered interlaced, the entire thing should be interlaced where there is motion. If only one portion of the spot is interlaced, I can only assume that something happened between you and the client.
3. Choosing a filed order should not be a crap shoot. The hardware that converts computer to tape has a very specific requirement for field order. Ask the editor who receives your material what he wants from you: lower first or upper first. If they say “odd” or “even” (bugger) tell them that DV is lower, so what do they call that, odd or even?
4. … but you don’t have to render interlaced at all. I haven’t done it in years. Rendering with no fields )progressive) is perfectly acceptable from a technical standpoint, and gives a look that I prefer, personally.
5. But as in #3, if you do render with fields, you must know which field order you’re choosing and why. It’s not a crap shoot (as in “try this, try that”). Always ask the editor what he/she needs from you. It’s your due diligence as a professional.
6. See if you can buy Chris and Trish Meyer’s Videosyncrasies disc.
Hope that helps …