Hmm. I see Microsoft has changed the layout of the .vcxproj file since MSVC2012.
In your project file I only found the following related to the assembler files:
<ItemGroup>
<None Include="..\..\..\..\Source\ThirdParty\AngelScript\Source\as_callfunc_arm_gcc.S" />
<MASM Include="..\..\..\..\Source\ThirdParty\AngelScript\Source\as_callfunc_arm_msvc.asm">
<FileType>Document</FileType>
</MASM>
<None Include="..\..\..\..\Source\ThirdParty\AngelScript\Source\as_callfunc_arm_xcode.S" />
<MASM Include="..\..\..\..\Source\ThirdParty\AngelScript\Source\as_callfunc_x64_msvc_asm.asm">
<FileType>Document</FileType>
</MASM>
</ItemGroup>
But there is no information on how the files should be built, much less the fact that only the arm version should be included in the ARM build and only the x64 version should be included in the x64 build. Perhaps MSVC2013 stores this information somewhere else?
In the MSVC2012 project file I have it looks like this:
<ItemGroup>
<CustomBuild Include="..\..\source\as_callfunc_x64_msvc_asm.asm">
<FileType>Document</FileType>
<Command Condition="'$(Configuration)|$(Platform)'=='Release|x64'">ml64.exe /c /nologo /Fo$(OutDir)as_callfunc_x64_msvc_asm.obj /W3 /Zi /Ta %(RootDir)%(Directory)\%(Filename)%(Extension)</Command>
<Outputs Condition="'$(Configuration)|$(Platform)'=='Release|x64'">$(OutDir)as_callfunc_x64_msvc_asm.obj;%(Outputs)</Outputs>
<Command Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">ml64.exe /c /nologo /Fo$(OutDir)as_callfunc_x64_msvc_asm.obj /W3 /Zi /Ta %(RootDir)%(Directory)\%(Filename)%(Extension)</Command>
<Outputs Condition="'$(Configuration)|$(Platform)'=='Debug|x64'">$(OutDir)as_callfunc_x64_msvc_asm.obj;%(Outputs)</Outputs>
</CustomBuild>
</ItemGroup>
(of course, I don't have a WinRT target in my project yet, so there is no compilation step for the arm assembler file.)
Have you checked that the as_callfunc_arm_msvc.obj is actually generated somewhere when compiling the library? If so, in what directory is it being generated? If it is not generated, check what command MSVC is actually running when getting to the assembler files (the project settings should have an option to visualize the command line).