When using folders (plugin), the batch tasks to be triggered must be referenced with an absolute path: while the task suggestion field works fine with a relative job path during configuration, the batch task is not properly configured in the later screens.

Let's consider a folder named aFolder with a job named aJob; that job has a batch task named aBatchTask

On http://.../jenkins/job/aFolder/job/aJob/configure :
Add an Invoke batch tasks post build step with two tasks, one absolute and one relative:

• Project: /aFolder/aJob
• Task: aBatchTask
• Project: aJob
• Task: aBatchTask

On http://.../jenkins/job/aFolder/job/aJob :
The "Downstream Tasks" lists:

• aFolder » aJob » aBatchTask
• Invalid entry: aJob » aBatchTask

An absolute job reference seems to be required here.