I don't have the CD version of the ORs as I have ready access to the books, but I've also noticed a problem with the book index. I've seen many instances where things have been "missed" in the index.
Not too long ago I was doing some heavy research on the 2nd Arkansas Cavalry (US), and I kept coming up with stuff that wasn't indexed. Or should I say, it wasn't indexed like I thought it would be. I first did the most logical thing of looking to see what volumes the regiment was mentioned in. And then I went to the individual volumes, found the page number, etc. And, of course, I found a lot of stuff that way. Unfortunately, I assumed that I had found everything.
Well, one day I decided to look under the commanding officer's name (Col. John E. Phelps). When I did that, I found quite a few additional reports, pieces of correspondence, etc., that were not indexed under the 2nd Arkansas Cavalry.....even though "2nd Arkansas Cavalry" appeared in the text of the document. Curious about this phenomenon, I decided to check under a bunch of other officers' names. Well, would you believe that I came up with about fifty pages of additional stuff?! I could not believe it.
While there were several instances where "2nd Arkansas Cavalry" was not mentioned in the text (and thus I should rightly not expect it to show up in the index), there were also many instances where it was part of the text and somehow just failed to make it into the index.
Of course now I wonder how much more stuff I've missed over the years. I suppose it just goes to show you that even a professional publication with dedicated editors can miss things. No one is infallible. I do wonder, though, if I would have run into the same thing with the CD or online version. I would like to do a comparison between the different versions, but I just haven't had time.