Boeing spent several billion dollars on R&D for the 777 and sells each plane for somewhere around $100-150 million. In constand dollar terms, I'm pretty sure they paid about the same amount for the 747. Aerospace R&D is expensive.

Once the R&D is completed, the per unit production costs for a CRV could be pretty low. However, unlike something like the 747 that was designed for mass production, when you're only talking about building 3 vehicles, the per unit costs can get pretty high. The CRV is intended for a 1 year on-orbit storage with fully automatic systems. Developing and certifying the software alone costs a fortune for manned space vehicles. A BSOD in a CRV would mean a dead crew.