So, Visual Studio 2013 comes with a new version of MSBuild i.e. MSBuild 12.0. Once installed, it changes the path so that the new version is used by default.
Looks like your solution compiles with visual studio 2012, you can either specify the full path to msbuild.exe such as
C:\Windows\Microsoft.NET\Framework\v4.0.30319\msbuild "path\solution.sln" /property:Configuration=Debug
or set the visual studio 2012 environment variables by running the following before executing msbuild
"%VS110COMNTOOLS%"\vsvars32.bat // VS2012 environment variables
EDIT: Using MSbuild 12.0 assemblies "C:\Program Files (x86)\MSBuild\12.0\Bin\" fixes the issue with the code Analysis bug.