The following is wrong and needs to be updated to match the new version string format:

copy {
    mkdir "$buildDir/native"
    mkdir "$buildDir/native/javapackager"
    from file("src/main/native/javapackager/win/javapackager.manifest")
    into file("$buildDir/native/javapackager")
    // FIXME: the following is wrong and needs to be fixed
    filter { line->
        line = line.replace("FXVERSION", "${RELEASE_VERSION}.${HUDSON_BUILD_NUMBER}");
    }
}

It should use the same 4 digit version as the DLL and EXE FileVersion parameter.