I think the difference in the sales of the two is due to the contents and pricing of them.
Though I'm not sure of the original pricing of the 30th anniversary CD, I doubt that even Disney attempted to sell it back then for $100. In addition to a likelier lower price, It did contain exclusive audio content (at the time, this was the first time the Mansion audio had been released on CD). It also had the "collectible" factor of being signed (on an insert) by Buddy Baker and X Atencio.
The new set, on the other hand, is $100 and, while beautifully produced, it has no audio content which can't be bought legitimately elsewhere for about $30 total. With the box, you're paying a $70 premium for a couple of pieces of art and a vinyl reproduction of one of the included CDs which - I'm willing to bet - most purchasers have no intent of ever actually playing. Don't get me wrong - I bought the box immediately and think it is gorgeous. However, I admit that I'm a bit of an object fetishist, so that's why I snapped it up. If I was just looking for the audio content, I would have bought just the individual CDs and not the box.
If it was Disney's primary intent to sell all of these boxes at a premium, they should have held back a month or two on the release of the individual CDs, then the box would have been seen as more of an 'exclusive' and it would have sold more quickly (it either would have sold out at the merchandise event where it was released, or at the D23 Expo immediately following it). As I understand it, though, the CDs were the planned releases and the special box was a relatively late in the game decision as a merchandise piece for the event. It also didn't help that - apparently - the people coordinating the Haunted Mansion merchandise event didn't seem very aware of the item - it wasn't listed in any of the advance promotion for the event as something that would be available, so attendees didn't know that it would be one of the offerings until the night of the event.
So, while it's a beautiful box, it just doesn't have that "need to have it" factor that the original CD release had.