it sounds like you need to up the antialiasing on the vector file under the Interpret Footage -> More Options -> Antialiasing: More Accurate
This will most likely take care of it, and i dont know why its not the default setting. I keep going into that dialog all the time for pdf and eps files. Especially if they contain raster images, they jump around like they are snapping to a pixelgrid and not properly resampel at subpixels.
Robert