UPDATE - I found that when i deleted the homepage, the options came back. I will re import the homepage and try again. This is very odd.
I am also seeing that if use a template i downloaded from my other pro site to populate a page or layout, if i navigate between pages etc whilst in cornerstone, i dont see the changes on the pages/layouts until i come out of cornerstone completely and go back in! It also doesnt update the page / layout names in the cornerstone menu until you exit cornerstone and go back in! Cornerstone seems very broken to me 
UPDATE 2 - Right. After messing around for quite a while. The fix that i think i have found is that you have to create firstly your homepage page and another blank page in CS and then go into Wordrpress Settings > Reading and set the static homepage and news page to be your 2 pages you have created for this purpose. THEN after you do this, you dont see the issues i mentioned above. I think you guys should look into this futher as i cant be the only one seeing this. I could also set up another blank fresh site if you would like to have a play so that you can see what i mean. Sorry for the long text.
Chris