You actually need to program the APIM based on your transmission (AT or MT)...can't remember the bit on the as-built but this definitely will fix your issue.
The software has nothing to do with the as-built changes...Sync 3 has 2 boards - the main one is the APIM which you interact with using Forscan and holds the as-built data and the smaller one which has the QNX image and it's what you see as a firmware.