Yesterday when I fought her, she wouldn't go to her second form. And when I fought her today, no matter how much I hit her she doesn't go down, its like she has infinite life. I'm using a fireaxe on her.

You'll probably have to start over...
Try re-loading a few times... although I bet you already have.

That is odd, but people have had glitches with Scarlet before. Once, she disappeared on me during her second form, but it went fine when I re-loaded. If re-loading doesn't work, it's possible you need a different copy of the game.
Try re-loading from your most recent save first, obviously, then try loading from a save a few slots back before you resort to starting completely over. If you play through again and have the same issues... your copy's bad, dude.

The first time i fought her, i had the same issue, but after a while i said, "you know, i dont care. I have a punching bag now, why am i so worried?" And with that, i proceded to beat the stuffing out of her until she changed. It took me an extra thirty or so minutes, but she DID end up changing for me. I suggest just thinking of something that rustles your jimmies, and pretending that it's all scarlet's fault. If that doesn't work, i.would recommend reloading.