Not a bug, but a configuration setting that needs to be changed. You need to go to Admin Layout (tiki-admin_layout.php) and activate Top bar for the CMS, Wiki and any other sections where it isn't already on. I don't see a setting for what you refer to as admin options, so I hope setting all to "on" will solve the problem.
Secondly - How do I stop it from displaying the contents of the left hand menu at the bottom right? - I've used the PHP layers menu for all my navigation, so the old menu is redundant.
That's the mnu_application_menu and is being displayed in a module. I'd go to the Admin Modules page and delete it from the Assigned Modules list.
By the way, I clicked on the "Read more" link on one of your articles and came upon a common problem with recent Tikis: you need to do a small database update, as there has been a database column name change. With phpMyAdmin or some other tool, submit these statements:
# fixed reserved word use in mysql alter table `tiki_articles` change `reads` `nbreads` int(14) default NULL ; alter table `tiki_submissions` change `reads` `nbreads` int(14) default NULL ;
That'll get your database table in sync with the templates and avoid the error.