Reproduction Steps

1. Install latest version of vcpkg (as of 3/28/18), and execute the installation steps as shown in the official github repo. In my case I installed it in D:\vcpkg-master
2. Install from vcpkg the boost library for windows x64 with the command: vcpkg install boost:x64-windows
3. Open my \VS15.6.4_VCPKG_CMAKE_BUG_REPRO folder with visual studio 15.6.4
   1. Double check that the CMakeSettings are loaded properly from the root of my project, and that they are not the default

Now you should be getting the following error message in the output window of cmake:

1> Command line: C:\PROGRAM FILES (X86)\MICROSOFT VISUAL STUDIO\2017\COMMUNITY\COMMON7\IDE\COMMONEXTENSIONS\MICROSOFT\CMAKE\CMake\bin\cmake.exe  -G "Visual Studio 15 2017 Win64" -DCMAKE_INSTALL_PREFIX:PATH="C:\Users\username\\CMakeBuilds\\f83620a4-25de-6d3d-940d-b8ce325208a2\\install\\x64-Debug"  -DCMAKE_TOOLCHAIN_FILE="D:/vcpkg-master/scripts/buildsystems/vcpkg.cmake"  -DCMAKE_CXX_COMPILER="C:/Program Files (x86)/Microsoft Visual Studio/2017/Community/VC/Tools/MSVC/14.13.26128/bin/HostX64/x64/cl.exe"  -DCMAKE_C_COMPILER="C:/Program Files (x86)/Microsoft Visual Studio/2017/Community/VC/Tools/MSVC/14.13.26128/bin/HostX64/x64/cl.exe"  -DCMAKE_CONFIGURATION_TYPES="Debug" "C:\Users\username\Desktop\repro"
1> Working directory: C:\Users\username\Desktop\repro\build\x64-Debug
1> -- Boost version: 1.66.0
1> FOUND BOOST
1> -- Configuring done
1> -- Generating done
1> -- Build files have been written to: C:/Users/username/Desktop/repro/build/x64-Debug
1> Starting CMake target info extraction ...
1> CMake server connection made.
1> Extracted includes paths.
1> Extracted CMake variables.
1> Extracted source files and headers.
1> Extracted global settings.
1> Extracted code model.
1> Extracted CTest info.
1> Collating data ...
1> Target info extraction done.
file=d:\vcpkg-master\scripts\buildsystems\vcpkg.cmake should not be rooted in a drive
Parameter name: file
Actual value was d:\vcpkg-master\scripts\buildsystems\vcpkg.cmake.file=d:\vcpkg-master\scripts\buildsystems\vcpkg.cmake should not be rooted in a drive
Parameter name: file
Actual value was d:\vcpkg-master\scripts\buildsystems\vcpkg.cmake.1> CMake generation canceled.

In the folder \cmake_manual_build you can see the project that I generated manually by calling cmake from powershell. This works properly with visual studio.