well after spending lot of time for this issue I finally found this thread.

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I have not yet solved the problem but at least it seems that I found the reason for it. So it seems like winscp was not guilty. The problem seems to be caused by sourceforge.net

The config.php file I chmodded to 666 was set to -rw-rw-rw- according to the terminal. The directores I chmodded to 777 were set to drwxrwxrwx according to the terminal. But doesnt that mean that permissions were set correctly. But the problem is that I still get error messages that the directory/file is not writable. And postnuke chmod check is still telling me, I have to chmod the config.php to 666 and some temporary directories to 777.

What permissions do you see if you list the directory from terminal?

I just used Winscp 3.76 and an older Version 3.1.0 to set file and folder permissions

This does not seem to work. I can change by right clicking ang choosing chmod 777 them and in winscp it seems that the permissions were changed. So far everything seems to be all right. Next to the file winscp shows that the permissions were changed to rwxrwxrwx. however the problem is that I still get the error message that the file is not writable and that I have to chmod config.php to 666 and some directories to 777 during my postnuke installation procedure.
How is that possible?