For my home page settings I have:
Visibility
Show in menus? "Ticked"
Show in search? "Ticked"
Who can view this page?
Inherit from parent page "Ticked"
Anyone
Logged-in users
Only these people (choose from list)
Who can edit this page?
Inherit from parent page "Ticked"
Anyone who can log-in to the CMS
Only these people (choose from list)
Manually specify a Google Sitemaps priority for this page (?)
Page Priority
1 - Most important
The settings for my other pages are the same except I have:
Manually specify a Google Sitemaps priority for this page (?)
Page Priority
Auto-set based on page depth
I thought it might have been a javascript conflict, so I tried removing all added code and reverting back to the last version before I lost my URLs, but that did not help. Also Google was able to scan the website and confirmed that the analytics code was ok (although I had to move it to with in the <head> for Google to confirm I owned the website.)
And just to show you, my website is http://www.englishediting.ch/
By the way, thanks heaps for trying to help :)