I\'m using SVN 1.6.3 and TortoiseSVN 1.6.6. Periodically when I do an update from the root of my project, SVN fails to pickup a newly added directory (added by a co-worker)
It sounds like you have a sparse working copy. Try svn update --set-depth infinity and see if that does it.
svn update --set-depth infinity
The equivalent in Tortoise is setting Update Depth to "Fully recursive" when you pull up the Update dialog.