Please attach a full session log file showing the problem (using the latest version of WinSCP). And a verbose FileZilla log too.
To generate the session log file, enable logging, log in to your server and do the operation and only the operation that causes the error. 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.
Preserve Remote Timestamp not working
I built a sftp server by using WS_FTP, i used file zilla as SFTP client, if I checked preserve timestamp option on file zilla, it is working fine. When I changed to use winscp, even if preserving timestamp option has been checked, the error message pop up.
Upload of file .. was successful, but error occurred while setting the permissions and/or timestamp. If the problem persists, turn off setting permissions or preserving timestamp. Alternatively you can turn on 'Ignore permission errors' option.
“The server does not support the operation”
I don't think that the SFTP server does not support preserving timestamp because of it works fine that if I use file zilla as SFTP client.