I found what the problem was, in the .vcxproj file. Nuget wasnt removing import for the older version:
<Import Project="$(NuGetPackageRoot)boost_thread-vc141.1.64.0.0\build\native\boost_thread-vc141.targets" Condition="Exists('$(NuGetPackageRoot)boost_thread-vc141.1.64.0.0\build\native\boost_thread-vc141.targets')" />
but if you manually remove the references to the old versions of the boost packages. it successfully builds libbitcoin-systems.lib
