I agree. The $100 million cap on settlements seems to relate only to the Pigford litigation (remember that?) and is not a generalized limitation on payments out of the Judgment Fund.
The payments in question cite 28 USC § 2414, which is authorized by the Judgement Fund law
31 USC § 1304 (a) Necessary amounts are appropriated to pay final judgments, awards, compromise settlements, and interest and costs specified in the judgments or otherwise authorized by law when (1) payment is not otherwise provided for; (2) payment is certified by the Secretary of the Treasury; and (3) the judgment, award, or settlement is payable (A) under section 2414, 2517, 2672, or 2677 of title 28;There's no mention of any cap on payments made from the Judgment Fund
Still, why wasn't the entire amount paid in a single payment? Why were the payments kept a penny below $100,000,000?