Space Engineers uses a different method, since they do not give the option for a server password, you must add a steam group ID to the config and invite users to that group so that they may join the server. Please submit a support ticket and we can get this done for you
Try selecting the "Clean SteamCMD Folder" option off and running the update! You may also try deleting mod data via FTP and running the update, a customer reported that helped him. Although it is also possible that a mod you are using is still not compatible with 1.06.