Please attach a full debug log file both for failed and successful session (using the latest version of WinSCP).
To generate log file, set
Session.DebugLogPath. Submit the log with your post as an attachment. You may want to remove data you consider sensitive though, such as host names, IP addresses, account names or file names. If you do not want to post the log publicly, you can mark the attachment as private.
I'm also having problems with timeouts. I'm using the latest beta version and calling WinSCP via the WinSCP Powershell Module (https://dotps1.github.io/WinSCP/). I get this message in the console:
Exception: Exception calling "SynchronizeDirectories" with "7" argument(s): "Timeout waiting for WinSCP to respond"
Please see the attached log file, and let me know if you need anything else.