It appears that it doesn't like large batch of files or folders during transfer. Today found out that the naming convention is somewhat funny because I got critical transfer error when a folder is transferred if the folder name isn't allowed. It says
must contain only ASCII letters (a-z,A-Z), digits (0-9), underscore, dot and dash.
Response: 553-Names must not start with a dot (.) or dash (-).
Response: 553-For additional info please visit:
Response: 553-See http://help.yahoo.com/help/us/webhosting/gftp/
E.g. I tried sending folder wp-backup-1.7, it failed because folder name wasn't OK I guess. I then created a folder named wpbackup17, have all files within it transferred then manually changed folder name to wp-backup-1.7, it was OK surprisingly. I have to ask Yahoo why?