Please attach a complete session log file both from GUI and the .NET assembly.
I have a powershell process using the winscp.net to load files to an SFTP site. It works just fine if files are under 32KB. Files over 32KB timeout... a 32KB filepart is left on the server each time.
File transfer through the GUI works fine; even larger files transfer in a snap. I'm not sure what's magic about 32KB... is there something like a raw site setting I need to try to modify?