I love your author's note. "This will be Royai...eventually." As your beta-reader, I know just how eventually that is. I am amused.
Oh, ahem. Sorry, I'm supposed to be reviewing the chapter, aren't I? Well, I beta-ed, so I'll be brief. This chapter gave you some of your biggest problems in your first draft and this revision takes care of them nicely. I like how you've captured the ambigious relationship between Roy and Winry here and you're doing an excellent job of building tension.
Now I just have to get cracking on Chapter 3.