Only now I have noticed that you refer to FTP protocol.
With FTP protocol in text/ascii mode, on upload, the client must convert the text file to CRLF format. The server then must convert the received file to its own format. It is possible that your server fails to do so.
Can you provide me a file you are having problems with?
Also what EOL characters have you configured on Environment tab of login dialog?
WinSCP breaks the line break while uploading using FTP.
Unix line break (\n) gets converted to (\r\n) on upload.