Hmm... Can't really say anything from here but if you could send an admin account to Cüneyt via PM he can debug it.

Have noticed the same, sometimes we need to refresh the site to see newly created modules, where they are really placed etc.
Some users also reports on similar issues with the menu system, sometimes it even deletes menu items. I guess those ajaxified areas need some more testing and love ...

Cheers Denis
The inspector just says 'success' every time I change the position. The admin page is working correctly and the layout_module table contents properly reflect the layout page but my shop home page doesn't change.
Is there some caching that needs invalidating after a layout change ?
I notice that console.log is permanently in the ajax success function in layout.js. Is this just done on admin pages or is console.log left in the code of the shop. ?

Yes David, it is supposed to auto save when you change the page section. Can you try to use the Inspect of your browser and see if Console gives any error?