B727 MISTAKENLY ALLOWS IMPROPER HAZMAT TO BE CARRIED ON FLT FROM LGA.

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JUST PRIOR TO DEP OF ACR FLT XXX; RAMP SUPVR CAME INTO COCKPIT WITH FORM FOR CAPT TO SIGN. IT WAS AN ACR FORM WITH OUR ACFT AND FLT NUMBER PROPERLY MADE OUT; STATING WE WERE CARRYING A BOX WITH A RADIOACTIVE SUBSTANCE AND IT HAD BEEN PLACED IN THE REAR CARGO. I READ THE INSTRUCTIONS ON THE ACR FORM; SIGNED IT AND FOLLOWED THE DIRECTIONS ON THE FORM DISPOSITION. ONE PART WENT TO THE RAMP PERSON AND THE OTHER WAS TO BE PUT IN THE FLT ENVELOPE TO BE RETAINED FOR 90 DAYS. IT DID NOT DAWN ON ME THAT THIS 'MIRRORING' PROC DID NOT APPLY TO THE ACR ACFT UNTIL OUR LNDG IN BOSTON; REALIZING THAT WE HAD CARRIED UNAUTH HAZMAT ON A SHUTTLE ACFT. WE AT THE SHUTTLE HAVE BEEN GIVEN A GREAT NUMBER OF OPERATIONAL CHANGES IN FORMS AND PROCS WITH NO FORMAL TRAINING. IT COMES IN BULLETINS OR REVISIONS WITH NO EXPLANATION EXCEPT THAT WE ARE ATTEMPTING TO 'MIRROR' AS MANY PROCS AS POSSIBLE. IT IS A DANGEROUS SIT TO HAVE STANDARDS THAT ARE CONTRARY TO EACH OTHER AT THE SAME AIRLINE. IT IS EVEN WORSE WHEN THEY ARE HAPHAZARDLY IMPLEMENTED AND IS VERY CONFUSING TO THE AVERAGE CREW MEMBER. ALSO LEADING TO MY CONFUSION IS THAT I HAD BEEN SCHEDULED FOR A320 SCHOOL ON AUG/XA/99 THAT WAS SUBSEQUENTLY POSTPONED. I HAD BEEN STUDYING ACR PROCS IN PREPARATION FOR THE TRANSITION AND IN THAT MATERIAL THIS WAS A PROPER PROC. THE RESPONSIBILITY TO CARRY THE BOX WAS SOLELY MINE. I MADE A MISTAKE; BUT I DO FEEL STRONGLY THAT I WAS SET UP BY THE CIRCUMSTANCES AND THAT I AM IN THE MIDDLE OF A TRANSITION OF OPERATING CERTIFICATES WITHOUT CLR DIRECTION.