I'm assuming that when you say "subdirectory" you're referring to a package. Please correct me if I'm wrong on this because it definitely makes a difference.
What version of CaseComplete are you using?
What change control system are you using? the built-in one or something else like Subversion, TFS etc?
Are you able to see the full 26 packages? What icon appears with those packages?
When someone else joins the project, do you see the .ucp files in the working folder that would correspond to the packages?
Any other intervening changes like restoring from a backup?
We may have to set up a web meeting to see exactly whats going on - there's a fair number of moving parts here.