The bug has been opened on https://bugs.launchpad.net/ubuntu/+source/epiphany-browser/+bug/123420

"Binary package hint: epiphany-browser

When editing the bookmarks, new topics wont show in the bookmark menu.
They do show in the bookmark edit window

ProblemType: Bug
Architecture: i386
Date: Sun Jul 1 20:18:13 2007
DistroRelease: Ubuntu 7.04
ExecutablePath: /usr/bin/epiphany
Package: epiphany-browser 2.18.1-0ubuntu1
...
Yes that seems to be the trick, however my categories were not empty
when I made them.
After adding one extra bookmark the category gets ¨activated¨
...
Import from mozilla and most categories wont show, adding one bookmark
to the category wil activate the category and now al bookmarks
originating from an other browser wil show up also. Removing the
bookmark added by epiphany wil remove the category from the bookmarklist
but it will remain ¨hidden¨ an can be activated again by adding a
bookmark again to the category.
It seems that imported bookmarks are treated different, so it seems an
import problem.
..."