I believe the old UI (dependencies) affects build order for Visual Studio, when building from within the IDE, for info. The new project configuration system embeds the references in each project file so that you can build from outside the IDE (whereas in previous versions, you could not, because you would not get automatic linking for dependencies, since dependencies were only done at the solution level).
There are also some issues with more complex projects in the new system; specifically, all resulting binary projects need to have explicit references to every dependent library to build correctly, whereas previously they could be effectively inherited from other dependent libraries. Same underlying cause, though.
Hope that helps.