I haven't seen the problem before. Do you see the file-size problem with all files? What is your SSH/SFTP server?
I would like to ask you to enable SFTP protocol logging
and send me the log file. After you enable the logging, let WinSCP list a directory that shows the invalid file sizes. If you are able to reproduce the "List index out of bounds (0)" on demand, try it too. Send the log file to my email address.
Thanks in advance for your cooperation.