We're using WinSCP to automate a few processes and find the first time a connection is established it must be done on the desktop, answer Yes to the requester to make the connection, after this scripts work.
That's not the right approach.
However, we had all our connections a fail as whatever cache tracked these certificates seemed to go astray and our automated processes (scripts) have been failing since December 1st.
Any idea why this happens?
That's too broad question. What configuration storage are you using? Registry or INI file? Can you attach a log file showing the problem?