One reason that could make the directory not being listed when trying to use is as a filter for a report is because there are multiple trees in CyReport Directory. The directory is meant to have a single main tree. To get this problem fixed, follow the steps below:
1) Make a backup of the CyTrack database.
2) Open CyReport Directory.
3) Identify which is the valid tree and which are the invalid(s) one(s):
4) Select each invalid tree and click Delete Tree button leaving only a single tree in the directory:
5) Click Save.
Originally from ticket #23465.