Firstly, what version of WinGate are you currently using? If it's not the latest version (6.6.1), then I recommend upgrading to ensure that the problem you are experiencing hasn't already been fixed.
If after upgrading the problem continues to occur, some packet capture would explain what's happening. Could you get a packet capture of this problem happening on your external interface facing the internet, and your internal interface facing the client. We will be able to compare these captures to see what data we are getting from the remote FTP server, and what data we are proxying to the client.
As packet captures are a tad big for the forum, can you send them to
support@qbik.com, thanks.