I do not know what could be wrong with your JCL. I noticed that there were some fixes added after the GA release concerning this:
002 13711425: CAN'T CONVERT EXTERNAL SYSIN
002 15869639: INCORRECT KSH GENERATED WHEN USING SYSIN IN PROC
002 15919377: JCL CONVERSION: IKJEFT01 RUNNING DSNTIAUL AND ITS SYSIN CONVERSION ERROR
003 16395341: DATASET NAME CONTAINING "BACKUP" IN SYSIN OF IDCAMS ISN'T CONVERTED CORRECTLY
003 16395313: ERROR IN CONVERTING SYSIN CONCATENATION FOR IDCAMS
003 16482629: SYSTSIN IS NOT TRANSLATED CORRECTLY FOR IKJEFT LANUNCHING NON SYSTEM PROGRAMS
003 16505306: SUBSEQUENT EXTERNAL SYSIN FILES IN SYSIN CONCATENATION SERIES ARE CONVERTED INCO
004 16671620: SUPPORT DYNAMIC SYSIN
004 16671597: SUPPORT FULL NAME SEARCHING FOR SYSIN
006 16834384: SUPPORT EXTERNAL SYSTSIN AND SYSTSIN OVERRD
If you have applied RP014 then these changes were included.
You will probably need to open an SR and provide the KSH you are getting in order to determine why.