When using the local build engine resource properties are only turned into PULSE_* environment variables if the resource is defined at project level.

If I have the following local resource file:

<resources>
  <resource name="doxygen"
        <property name="doxygen.bin" value="C:\\Program Files\\doxygen\\bin\\doxygen.exe"/>
  </resource>
</resources>

then this doesn't define PULSE_DOXYGEN_BIN:

<project defaultRecipe="doxygen">
  <recipe name="doxygen">
    <resource name="doxygen"/> <---- If this is defined inside <recipe>, PULSE_DOXYGEN_BIN is not defined
    <executable name="Build doxygen" exe="${ruby.bin}">
      <arg>common/doxygen-internal/build.rb</arg>
    </executable>
  </recipe>
</project>

whereas this causes it to get defined.

<project defaultRecipe="doxygen">
    <resource name="doxygen"/> <---- If resource placed here, PULSE_DOXYGEN_BIN is defined
    <recipe name="doxygen">
      <executable name="Build doxygen" exe="${ruby.bin}">
        <arg>common/doxygen-internal/build.rb</arg>
      </executable>
  </recipe>
</project>

Also, as far as I can tell putting <resource> at <project> level is an undocumented feature.