To simplify checking out a list of modules (directories) we defined an alias for this list of modules in the CVS modules file on the server. In general fetching of the files with the Jenkins CVS PlugIn works fine using the alias, but there are several empty directories (all files that once existed in these directories have been deleted from CVS) which remain after checkout/update. When we don't use the alias, but specify the modules explicitly, the empty folders get pruned correctly.
From my point of view it is possible that this bug has been introdcued with the changes related to #20317 (https://issues.jenkins-ci.org/browse/JENKINS-20317)
Feel free to contact me, if you need further information.