I've experienced the same issue having the latest version of WIX installed (3.9) and NetBeans 7.4.
In my case this was due to a string comparison problem in the file "jfx-impl.xml" in the nbproject folder. What you have to do is editing this file (clicking on the link provided by the error message in the NetBeans output console) and changing the target "-check-WiX-presence" into this:
<target name="-check-WiX-presence" depends="-check-native-bundling-type" if="need.WiX.presence">
<local name="exec-output"/>
<local name="exec-error"/>
<local name="exec-result"/>
<exec executable="candle" outputproperty="exec-output" failifexecutionfails="false" errorproperty="exec-error" resultproperty="exec-result">
<arg value="-?"/>
</exec>
<echo message="exec-output:${exec-output}" level="verbose"/>
<echo message="exec-error:${exec-error}" level="verbose"/>
<echo message="exec-result:${exec-result}" level="verbose"/>
<condition property="missing.WiX">
<not><and>
<contains string="${exec-output}" substring="Windows Installer XML" casesensitive="false"/>
<not><contains string="${exec-output}" substring="Windows Installer Xml Compiler version 1"/></not>
<not><contains string="${exec-output}" substring="Windows Installer Xml Compiler version 2"/></not>
</and></not>
</condition>
</target>