Do you have the problem when opening file from remote panel or also when opening a local copy?
If also with the local copy, can you attach the file here, so I can test myself? Please ZIP the file first to make sure, it does not get altered while uploaded. If you do not want to post it publicly, you can email it to me.

Windows 8 WinSCP v.5.1 SFTP protocol.

Created by PHP script text file (27kB with 256 lines) WinSCP opens only with 77 lines. All the changes WinSCP saves correctly but after the transfer to my local computer still is showing only 77 lines. I have tried text mode and binary mode. Opening it under Windows using Notepad shows all 256 lines. This is only an example. Any idea how to change the setup? I haven't had any problem with it in ver. 4.