Why does the time becom 00:00 and the size different when copying from local disk to linux filesystem?
Time 00:00 is displayed for SCP protocol, when 'ls -la' contains only date for particular file. So it may not mean that time is 00:00, but that time is unknown. Check the log file for what server lists. Also you may try SFTP protocol instead of SCP. With SFTP this never happens.
Size may differ, if you transfered file using text-mode, because line-endings has 2 bytes on Windows, while only 1 byte on UNIX.