It's possible with some FTP servers.
See "Timestamp precision"
To confirm, check in WinSCP GUI shows "times" of the affected files in file panel.
If that does not match your scenario, please attach a full session log file showing the problem (using the latest version of WinSCP).
To generate the session log file, use
/log=path_to_log_file command-line argument
. Submit the log with your post as an attachment. Note that passwords and passphrases not stored in the log. You may want to remove other data you consider sensitive though, such as host names, IP addresses, account names or file names (unless they are relevant to the problem). If you do not want to post the log publicly, you can mark the attachment as private.