Strange, because I can only reproduce the issue you describe if I do have a matching entry. Please double check that - you should look in the Passwords section for entries with your server Name or IP Address and delete them.
In addition, turn off the 'Store passwords in Keychain' option in the Interface panel of the Yummy FTP Preferences. Then we can be sure Keychain is not being used, and also when this option is off then Yummy stores any entered password into the Bookmark file itself. So if you empty the password it will definitely be empty in the Bookmark.