The purpose of the Judgement Fund (31 USC § 1304) is “to pay final judgments, awards, compromise settlements, and interest and costs specified in the judgments or otherwise authorized by law”
But it is not a fund, like a pot of money that sits there. It is an accounting trick -- when they need money (for the judgments, settlements, etc.), they are authorized to put money in this "fund" and make payouts from there.
They are using this for no other reason than to circumvent Congress on the funding of Obamacare, after Congress has told them No. More. Money.
And who TF knows where the money is actually coming from.