Then it's probably not related to WinSCP update, but rather something has changed about the servers at the same time.
Are the servers public? Can you share their hostname? (at least privately?)

I've had the problem for a while. I think the problem started when I updated from WinSCP 6.5.1 to WinSCP 6.5.3. I'm currently using WinSCP 6.5.5

PuTTY is version 0.83

I just downgraded to WinSCP 6.5 and the problem still exists.

Thanks for your report. To what version did you update? What version were you using before? If you downgrade back, does the problem go away? What version of PuTTY are you using?

After a recent WinSCP update whenever I click on the "Open session in PuTTY" button I get the "PuTTY Security Alert" popup:


If I click on Yes I still get the same "PuTTY Security Alert" popup the next time I click on the "Open session in PuTTY" button. It never updates PuTTY's cache with the key.

This happens for 2 of my servers. But not the other 3 servers.
This happens if I'm connected in WinSCP as root or an admin user.