I recently had this problem too. Just set the SSH Host keys on all systems in the cluster to the same key if possible. You lose a little security, but hosts in a clusters are supposed to be the same anyways.
How / where can I put the StrictHostKeyChecking=no in the .ini file. I'm using winSCP 3.8.0 (build 312).
I need this as the server i try to connect to is in a cluster and every machine has its own hostkey. Hope to hear from anyone.