I suspect JES2 won't end normally because it's waiting for the card reader to become ready. Do a $DU after a regular $PJES2. If I'm right, it'll show RDR1 DRAINING.
What I do for this is have a file on OPERATOR's A-disk named EOJ JCL, containing a single line of // . Then, from OPERATOR, do SPOOL PUN MVS and PUNCH EOJ JCL. JES2 will report RDR1 DRAINED (might also say RDR1 SKIPPING FOR JOB CARD) and end normally.