I've found exactly the same thing every time I've searched - when selecting "flight and hotel" for the whole trip you can get some fantastic deals. However if you "add" the hotel during a normal flight booking or indeed choose to have a hotel for only part of the trip when making a "flight and hotel" booking it reverts to a standard flight booking and adds the hotel on separately.

I think that you don't get the combination discounts when the hotel is added on top of a flight rather than a "package" deal