thanks Toby!
After a lot of search I finally found your post. I was also using
require('./wp-blog-header.php');
in an external php page for ajax processing and your ‘fix’ worked like a charm!
Thanks again man!
The same thing happened to me.
I tried the fix Cliveloseby posted earlier. It did showed those ‘invisible’ categories again, but if I tried to give them the same parent as before they would disappear from the list again…
very strange…