I've exactly the same problem. I'm using WinSCP Version 4.1.8 (Build 415) on Windwos XP Professional SP2.
When transfering files from local to remote with FTP passive mode nearly every file is truncated even the small ones (1 to 4 kB) regardless of the transfer mode (binary or text).
Can you send me an email, so I can send you back a debug version of WinSCP to track the problem? Please include 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.