In scripting, do not rely on GUI configuration. On the contrary, you should isolate the script from GUI configuration:
https://winscp.net/eng/docs/scripting#configuration

To enable logging in scripting, use /log command-line parameter:
https://winscp.net/eng/docs/commandline#logging

The session log in Winscp preferences is getting unchecked automatically. I reenable it back and again it gets unchecked. Due to this the exit codes are not getting displayed in most my scripts. Not sure what the issue is. Any suggestions?