To elaborate on Anders' point, you should see either "atkpython" or "atkpython_exec" and you can kill this process without "harming" VNL. Thanks for providing information about the operating system. Could you please also write which version of VNL/ATK you are using? I think you have a hit a bug which has been fixed in the upcoming release, but I would like some more information to be sure that it is indeed the same problem.
Also, just to clarify: Does the Job Manager act as if the job is finished, but the job continues running when you look at top? Or is the Job Manager itself unresponsive?