I have what may be a similar problem with one show in particular that does the same thing. If I look into the To Do List, it always shows that it is scheduled to record every episode of this show (SP is NEW ONLY). However, only the new episodes record in the end.
It appears to do with the programming information. The show information always seems generic initially, so the TiVo shows it to record in the To Do List. Then, the program information seems to be updated prior to the airings, so only the new episodes actually record.
Checking other things like Wish Lists, as suggested by steve614, may also be a solution.
TiVo Roamio Pro Lifetime ∙ TiVo Mini Lifetime
XBOX LIVE: fiftyfootfang