I recently discovered that TSA and CBP MCL APIS info on our crew does not match. We had been on a TSA TFSSP and followed all the MCL submission protocols with the ediapis.exe program. We opted out of the TFSSP in 2005 since they changed the definition of 12,500 lbs aircraft (no longer inclusive). With CBP's setup of eAPIS in the fall of 2005 we started using that website exclusively. Since then we had a pilot leave and hired a new pilot. I made all the changes to the MCL on the eAPIS website. We recently got a error message on a recent APIS submission from TSA and I requested a copy of our current MCL. It still had the old pilot and did not have the new pilot. Is this going to trigger a penalty action? Did I miss something? Should we still be using the ediapis.exe program for MCLs or just https://eapis.cbp.dhs.gov/ ? This site shows our correct info.