OK, This should be impossible but it is happening.

I have redone categories, deleting most, renaming some and adding new. I have also updated the wrapper and main templates and uploaded them correctly. Whilst logged in I see all of the changes I have made and it is perfect. However, the minute I log out I lose the majority of changes. 

Yes, I have deleted my browser cache, and in fact gone on to another computer to check it.

Yes, I have regenerated - several times

Yes, I definitely uploaded the changes - I can see them when logged in

Here are screen shots:  The first is whilst I am logged in, the second logged-out