A text file that I was transferring had that last few hundred bytes turned into random binary gibberish.
The remote server is AIX version 5.3
I am using a shortcut with the "Target" =
"C:\Program Files\WinSCP\WinSCP.exe" /ini="C:\MyStuff\Config Files (irreplaceable)\WinSCP\WinSCP-dev_env.ini" "sftp://MY_USER:MY_PASS@MY_SERVER/apps/control/"
to log in.
The .ini file just has the generic settings for a dev type environment.