Sometimes when adding FTP accounts the user does not have permissions to write to their wwwroot folder.
Check that in the FTP account settings in Helm, that the account has Read and Write boxes enabled. If so, then check if you have installed FrontPage extensions on this domain. Using FTP with FrontPage can cause errors in the FrontPage extensions. Therefore Windows removes FTP access to the wwwroot folder when FP extensions are installed.
Due to this issue with FrontPage, there is currently no way of guaranteeing that domains with FP and MS FTP on will work correctly.