i found that sometimes i have that problem as well when i render out the finished roto with fields. since you cant see each individual field in the timeline it looks ok on ram preview. but when you render with fields there is shifting, because your mask is not lining up (because you did not roto each field.)
usually we deinterlace the footage first and work with that footage. or ill take the original 29.97 clip and put it in a 59.94 comp and roto it in there (now i see every field.) then ill put that comp back into a 29.97 comp and render.
hope that can help you figure a solution.
-frank