One of the systematic changes in MoR is that things which are sufficiently powerful are artifacts, and things which are artifacts are sufficiently powerful: The Marauder's Map was originally devised by Slytherin as part of the creation of Hogwarts and only slightly twisted by the Marauders (Ch. 25), and the Cloak of Invisibility is now in a class of its own compared to standard invisibility cloaks or Disillusionment (Ch. 54).
Rowling, of course, wrote that thing with Moody's eye before she decided the Cloak of Invisibility was a major artifact. So if Moody's eye can still see through it in MoR, it's going to be because either Moody's eye is also a major artifact, or, more likely, a specialized artifact devoted to seeing through invisibility (a specialized, specific artifact can defeat a generally more powerful artifact if the specialization is narrow enough).
Wow... I had imagined that Moody lost his eye in a fight or something -- but it would be way more awesome if he cut it out intentionally, to replace it with an eye more suited for the hunt.
[Update: and now there's a fifth discussion thread, which you should probably use in preference to this one. Later update: and a sixth -- in the discussion section, which is where these threads are living for now on. Also: tag for HP threads in the main section, and tag for HP threads in the discussion section.]
The third discussion thread is above 500 comments now, just like the others, so it's time for a new one. Predecessors: one, two, three. For anyone who's been on Mars and doesn't know what this is about: it's Eliezer's remarkable Harry Potter fanfic.
Spoiler warning and helpful suggestion (copied from those in the earlier threads):
Spoiler Warning: this thread contains unrot13'd spoilers for Harry Potter and the Methods of Rationality up to the current chapter and for the original Harry Potter series. Please continue to use rot13 for spoilers to other works of fiction, or if you have insider knowledge of future chapters of Harry Potter and the Methods of Rationality.
A suggestion: mention at the top of your comment which chapter you're commenting on, or what chapter you're up to, so that people can understand the context of your comment even after more chapters have been posted. This can also help people avoid reading spoilers for a new chapter before they realize that there is a new chapter.