Well, it's probably a mix of feeling confident in it's ability to answer the Final Jeopardy question (based on previous performances), along with wanting to maximize its score as much as possible, especially considering it has to count that it is a 2 game average, not just one.

I thought the engineers might be trying to make its score end in a particular number if Watson was correct, as a sort of Easter egg.

It looked like it might be 658, which spells "BSG" upside-down on a calculator. Now that would be a great moment in geek history, hiding a Battlestar Galactica reference with a calculator message using a computer on Jeopardy!

Alas, the number it was betting towards was 37,628, which (at the risk of paraphrasing Hardy) is not a very interesting number. Or is it?!

Because there was still a slim chance that it thought it was right. If it's well ahead, it shouldn't bet $0 unless it knows with absolutely confidence that it's wrong.