You probably depend on your configuration of WinSCP. Note that when using registry as configuration storage, the settings are accessible only for your Windows account. When the script is run from Windows Scheduler, SSIS, DTS or other automation service, it is typically run under different (service) account that cannot access your configuration.

Possible consequences are:

• The script “hangs” because the host key (SFTP or SCP) or certificate (FTPS) is not known by the service’s account and WinSCP asks for its verification.
• The connection fails, because your script depends on stored session, which is not known by the service’s account.
• Environment variables referenced in script are not resolved, because they are not set by the service’s account.

Solutions:

• Make sure the host key or certificate is verified under the service’s account. With SSH you can also specify fingerprint of expected hostkey in the script.
• Transfer the stored session (or other settings) to the service’s account.
• or Use INI file instead of registry to store the configuration. The INI file can be accessed by all accounts.

When dealing with SSIS see also guide to SFTP task in SSIS.