Certain SFTP (ssh) servers will have a path that includes the user name in it such as the following examples of a user logged in on vshell:
username:/
username:/pub
In this scenario, go to the site manager, and change your 'remote startup folder' to be the startup directory you want to start in.
For example:
/
or
/pub/
Be sure to click the 'abs' button also. This will temporarily take care of certain path problems that may be experienced when queuing or scheduling files for older versions of Core FTP. There should be a fix to this in the near future.