To my understanding, Boeing has already admited that there's some sort of software fault... even before the black box was found. Which suggests they already knew something was wrong with this type of plane, yet decided to save a few pennies for their precious shareholders.
The software tweaks were discussed in the emergency AD issued after the Lion Air crash. They are small adjustments. The mandatory implementation date was April and no grounding was issued before implementation so it was never considered a flight safety issue due to the existing procedures in place.