The season in question (Season 28) would have been the only time within that period, if not ever, that there was a two-week break. Every other year it was one week, if at all. I figured that it was due to the tournament games amongst the Power Six conferences. However, while they were played during the day, that would have been an issue earlier in the week. Moreover, those games would have been on ESPN and the like, not on network television (until the weekend or weeknights maybe).
Plus, 1999-2000 was the year Bob had surgery which resulted in the loss of nearly 2 dozen tapings. There was a week-long break very early in the 2000 segment of Season 28 in addition to those two consecutive weeks in March