Batch Create

When I import a spreadsheet of users with batch create, the sites created are in the wrong directory and I get an error message saying ‘no input file specified’. Forinstance the main site on which I have multisite installed in when I use batch create it creates the site, example but misses out the ‘wordpress’ directory. When create sites via the add site function in WP, everything is fine. Please help ASAP because its driving me mad!!!!! Please – Regards Paul