I think the results of https://bugreports.qt-project.org/browse/QTBUG-30373 (definitely could be wrong about this, it was merged in on 2014-09-30 I think)
caused the vcxproj generation to no longer create custom build steps like:

    <CustomBuild Include="FILE.hpp">
      <AdditionalInputs Condition="&apos;$(Configuration)|$(Platform)&apos;==&apos;Release|x64&apos;">FILE.hpp;%(AdditionalInputs)</AdditionalInputs>
      <Command Condition="&apos;$(Configuration)|$(Platform)&apos;==&apos;Release|x64&apos;">C:\Qt\Qt5.4.0_Beta_S\5.4\msvc2013_64\bin\moc.exe ...

in the latest snapshot it simply creates:

  <ItemGroup>
    <ClInclude Include="FILE.hpp" />
  </ItemGroup>

my qmake step is:
"qmake -spec win32-msvc2013 -tp vc -r"

The 5.4-alpha did not show this behaviour.

Snapshot: qt-opensource-windows-x86-msvc2013_64-5.4.0-beta_2014-10-01_10-00-08-30

Update: See attached file for example .pro.