Basically, the Post Office leadership could not understand why someone would buy a PO franchise. It's a substantial amount of money up front, and people aren't allowed to buy multiple franchises, so every PO was an owner/operator position. Essentially people were "buying a job".
The people in leadership couldn't understand why someone would buy the opportunity to work long hours at a retail position and end up hopefully clearing a middle class salary at the end of the year. They assumed that there must be a real reason why people were signing up and the real reason was to put their hands in the till.
So they ended up assuming the postmasters were stealing, and the purpose of the accounting software was to detect the fraud so it could be prosecuted. When the accounting software started finding vast amounts of missing funds, they ignored questions about the software because it was working as intended. I bet if the opposite had happened, and it found very little fraud, they would have become suspicious of the software because their priors were that the postmasters were a bunch of thieves.