Even with the newest Holman Bible update (today's 2/12/09) I have noticed that the reference links that do not have the book name in front of them do not link.

e.g. Jn 1:15 (links fine), 2:5, 5:4 (does not), Act 3:12 (again fine)

The ones that do not link are grayed out. I am sure you are already aware of this. But just wanted to say it in case.

Yes, we're definitely aware of this. This is very prevalent in the MacArthur notes as well. We'll need to beef up an already complex parsing routine to pick those references up. Eventually, we'll get all the references :)