I'm sure that some of those who have given evidence to the inquiry didn't know there was a problem, and at least one of those who was aware of problems appears to have been unaware of PO's prosecution spree. However, a lot of them seem to be suffering selective amnesia. The most embarrassing in some respects is the solicitor who sent a triumphal email when Seema Misra was convicted who now claims that he didn't write the email, he doesn't know who did and he never knew any of the people to whom the email was addressed.
The helpline was operated by Fujitsu. As you say, part of the problem was overt racism - "another Patel on the fiddle". Even when frontline support staff did escalate problems, they often weren't investigated properly. Two examples involving Ann Chambers (who gave evidence for the PO in the Lee Castleton case).
First involved a customer coming in to buy $1,000. Horizon recorded one half of the transaction (the foreign currency going out) but not the other half (the cash coming in). As a result, the subpostmaster's accounts showed a false surplus of around £500. Fujitsu picked this up and try to fix it by inserting a new transaction (something Post Office repeatedly said was not possible but was, in fact, routine). Following this correction, the subpostmaster's accounts showed a shortfall of $1,000 - the cash was now correct but the branch was now shown as having more foreign currency than it should. It should have been obvious that they had got the correction wrong, but Ann Chambers concluded that this was a genuine loss at the branch and informed PO.
Second was an issue where a subpostmaster was having a problem that was causing losses at one of his sites. Unusually, a trainer went to the branch to help. They found that the subpostmaster was not doing anything wrong and reported that they had seen the error happen. Next, auditors visited. Unusually, they also reported that the subpostmaster was doing nothing wrong and that they had also seen the error happen. This report ended up with Ann Chambers. After spending 1 hour 16 minutes investigating, she closed the case saying that there was nothing wrong with the system and that the problem was user error.
Part of the problem is that the bonuses for both auditors and investigators depended on the amount they recovered from subpostmasters, so they were incentivised to find shortfalls and not to investigate them properly. From the evidence available, it seems that Post Office investigators had long thought that many subpostmasters were fiddling their accounts, so the "evidence" from Horizon simply backed up their existing belief. Indeed, from the evidence given to the inquiry, it seems that at least some of the investigators still don't accept that the subpostmasters were innocent. One particularly nasty example had to be repeatedly stopped from making accusations against an ex-subpostmaster's husband without any evidence.