And the issue is not just that the Post Office knew, but that they were also in charge of the prosecutions.
Private prosecution itself is on trial here, IMO (IANAL but this opinion would not be unusual among lawyers from what I have read)
Edit to add link:
https://www.computerweekly.com/news/252485328/MPs-to-examine...
The data that I can see shows that 76 subpostmasters were prosecuted in Scotland which doesn't seem completely wacky out of line with the rest of the UK.
Do we know how many Scottish prosecutions did not go forward with the fiscal?
The fundamental issue here is that it is likely that the Post Office on the one hand knew of the problems with the code and on the other still continued its prosecutions (based on its longstanding reputation). The fact that in England and Wales they could get away with that without systematic scrutiny surely only sways the chances of cases succeeding elsewhere. There was evidence from Horizon identifying the frauds, after all, and they had been successfully prosecuted.
I imagine much has changed; but I'm quite sure that the PO is still not an ordinary business, like a courier service. They are an arm of government.
The bit that is not "ordinary" is Royal Mail.
Whether they notified the Post Office or not though, the Post Office certainly knew. They not only shared emails about the problem within the organisation, they engaged in a cover up.
There’s a good BBC Panorama documentary on the scandal that was released more than a year ago.