Messages are ordered newest-to-oldest in this index. The newest threads will be at the top of this page, the oldest will be at the bottom.
Within a single thread, the first mail note is the START of the thread; the notes following that are in the chronological order of when they were received. So globally, newest messages are at the top, but within a thread, the oldest (the start of the thread) is at the top.
If you think about it, it is confusing. Just go with the flow and everything will be all right.