I don't know if this helps, but...
* I've gone through the config.xml file and compared it to an old backup that worked as expected - I can't see any differences that I can not explain.
* I've also compared the config.xml files for a project that reports the right number of tests and one that reports the wrong number. Obviously there are differences, but I can't see anything that might be related to the the way JUnit tests are reported.
* There is nothing in the Jenkins logs that indicates a problem with the rogue project
* There are two lines in the console output that read:
[JENKINS] Recording test results
Although this was always the case
Is there some other place I should be looking to determine what the problem might be?