Html publisher plugin for Jenkins not triggering Doxygen to create documents

Question

I am able to run Doxygen via the Doxygen GUI frontend and generate the documentation as expected. When I configure this to run in Jenkins, the console output from my build suggests that doxygen is running:

[htmlpublisher] Archiving HTML reports...
[htmlpublisher] Archiving at PROJECT level 
         C:\Doxygen\html to 
         C:\Jenkins\jobs\GIT_MASTER\htmlreports\GIT_MASTER_Doxygen_Documentation
Finished: SUCCESS

However when I check the OUTPUT_DIRECTORY it is empty.

My version of Jenkins is 1.542, the html publisher plugin is 1.3 and Doxygen is 1.8.6

I'm wondering if I have missed something in Jenkins configuration but I can't find anything else. As always any help is appreciated.

BTW, the Jenkins Doxygen plugin works as expected to generate html reports.

Thanks