"Prefer standard def." will record on a HD channel if the same show is not simulcast on an SD channel at the same time (same episode, same start time and same duration).
If you want a series to only record on an SD channel you should use the "Only standard def." setting. Just be aware that if for some reason the show only airs on a HD channel it won't record (where "Prefer standard def." would have).
Sunday's Doctor Who on ABC and ABC HD is listed as 50 minutes duration, but on ABC ME it is listed as 45 minutes duration. So they are seen as 2 different airings of that episode... but both "new" episodes because neither will be finished before the other one starts.
In cases like this I would set the series to "Only high def." so it won't ever record on ABC ME or ABC.