OK, but you still didn't tell us how exactly this is connected to WinSCP. Do you download the files using WinSCP? With the ZIP files, do you download them the same way? Are you using a binary mode in WinSCP? Can post a session log file? Did you try using any other client using the same protocol? Does it behave differently?
When my customers load a large text file on my server and I download it using WinSCP the file will have Chinese charters replacing text charters. The only solution I have found is having my customers zip the files before uploading to my server.