old man is correct, as the Levush says that the 247 year cycle is not exact, and does not repeat itself precisely. The Biur Halacha (Siman 428) lists the years were the Tur’s calendar is not exact, and the corrections.
The loss of a day every hundred years is not related at all to the calendar. The calendar is based on Tekufas Rav Ada, which is only slightly off (as mentioned by zahavasdad). For Tal U’matar we use Tekufas Shmuel, which is indeed off by 3 days every 400 years.