The failing module is 12897713 which still has your stock firmware installed. The working module 12897980 most likely had been updated using our USB boot method. So most likely it was working with your stock firmware.
The failing module also fails if no USB drive is involved. Or is the output below to be expected from a module with factory firmware?
MMC: no card present
switch to partitions #0, OK
mmc0(part 0) is current device
** Unrecognized filesystem type **
Do you think it is worth the effort downgrading the working module to see if it fails with stock firmware?
For initial flashing we use a Toradex Easy Installer thumbdrive with our image as explained here:
We use this method because it neither requires a display, serial interface nor network interface. Our manufacturing just plugs in the thumb drive, powers the system on and waits until it has been flashed. This works for most modules but we found a few which do not as explained above.