Debugging sure is difficult in here =) I'm usually using a lot of printErr's to find out what goes wrong(i'm a JS user).
Aside from that, it's difficult to say, what have gone wrong in your case without looking at actual code. But i'll try First impression - it's really matter of accuracy, try to use double, like elysius have already said. Timeout is unlikely, since you've passed both complete files tests, and they are bigger. And comma conversion doesn't make much of a difference in this scale.