All DV footage (NTSC and PAL) is captured lower field first. Make certain your Premiere project settings are ALL lower field first. In AE, you should definitely interpret the footage (in the project window) lower field as well.
When you render the final Quicktime, the editor needs to tell you what the field order of his/her system is. If it’s DV based, it will be lower field first. In PAL land, many higher end devices and capture cards (like Decklink, Kona etc) use upper field first.