I know this was posted a long time ago but I came across the same problem and in case it might help someone else, I solved it by using the "-W block=true" qsub option for PBS systems(i think the problem arises because "the qsub command exits after returning the ID of the new job" and not after completing the task)

In reply to Re^3: submitting job to a queue by Anonymous Monk
in thread submitting job to a queue by mjr1n1

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