Actually, thanks for the answer, i didn't give enough information in the original post. I eventually found it. When you run WinSCP with a /ini you can change the .ini file used by WinSCP, i didn't know that. I presume running WinSCP.exe would pick up the WinSCP.ini in the same folder.
In our case, we were setting it to another instance of the initialisation file. It was a large script, I was making the above presumption. Now i know you should set it with the /ini. I basically picked up DOS shell and WinSCP usage in the last day and a half.
Thanks

If you have problem with a script, you need to modify the script, not GUI settings.
See https://winscp.net/eng/docs/message_preserve_time_perm#scripting

Hello

I know this is a common error, and i've searched different forums and tried different options proposed. I've tried :"turn off Set permissions and Preserve timestamp options or turn on Ignore permission errors.".
I create a file full of PUT commands, and then run the WINSCP command on the file in simple terms. But quite often the WINSCP quits before completing the file with the error.

I have the error : was successful, but error occurred while setting the permissions and/or timestamp. If the problem persists, turn on 'Ignore permission errors' option.