So, is this bug fixed? 13 years already and I got the same error. The file keeps uploading way past 100% and never finishes. The exact same problem as stated by the OP.
Only completely closing winscp works, not even disconnecting the session.
Same problem, same answer: Can you send me an email, so I can send you back a debug version of WinSCP to track the problem? Please include a link back to this topic in your email. Also note in this topic that you have sent the email. Thanks.
You will find my address (if you log in) in my forum profile.