custom permalinks throw up a 404

Today we added some domains into the 'block domains' option

Our custom permalinks (/%postname%/) stopped working - they throw up 404.

If we switch to 'default or 'day and name' it works works ok again

Amazingly, if we then switch to the custom setting, they work too...

We recreated the .htaccess file, but no impact

How do we get back to custom permalinks working on creation of a new blog?