Got it, thanks - the link on stored sites/scripting helped me out.
And thanks for the recommendation on switching to the WinSCP.NET assembly. I'll look into that. As a side note, I went down the existing route based on this blog post by Tim Mitchell: https://www.timmitchell.net/post/2015/08/03/accessing-sftp-with-ssis/

Please attach a full session log file showing the problem (using the latest version of WinSCP).



Though for now, I will guess that you open a stored site in your script and that site has some local folder set (it's not recommended to use stored sites in scripting).

Btw, as you use C#, you should switch to WinSCP .NET assembly:
https://winscp.net/eng/docs/library
https://winscp.net/eng/docs/library_ssis

I have the following code to start the WinSCP process - this is being called in an SSIS C# script component:

Process winscp = new Process();
string logName = Dts.Variables["User::XMLLogLocation"].Value.ToString();

// Set the executable path and download directory
winscp.StartInfo.FileName = Dts.Variables["$Package::pWinSCPLocation"].Value.ToString();
winscp.StartInfo.WorkingDirectory = Dts.Variables["$Package::pDownloadDir"].Value.ToString();

// Set static execution options (these should not need to change)
winscp.StartInfo.UseShellExecute = false;
winscp.StartInfo.RedirectStandardInput = true;
winscp.StartInfo.RedirectStandardOutput = true;
winscp.StartInfo.CreateNoWindow = true;
winscp.StartInfo.Arguments = "/xmllog=\"" + logName + "\"";

Then the program runs a "synchronize local..." command to grab the appropriate files.

The issue I'm having is that the sync copies the new files to a directory that is different than what I've set in winscp.StartInfo.WorkingDirectory = Dts.Variables["$Package::pDownloadDir"].Value.ToString();

Any ideas on where/how the directory is changing? It goes 1 level deeper in the folder structure than I am specifying.