This but is a side effect of bug 2966919.
Scenario: an eclipse project is in a clearcase snapshot view (project files and java sources).
Compiled files are located in a linked folder out of the snapshot view.
Result: directories created in the linked folder are displayed in the "Private files" view.
Environment: Win XP, Eclipse 3.5 SR2 and clearcase plugin V2.2.2.
Thanks for using the Eclipse ClearCase plugin and reporting this bug. We'll have a look at this ASAP.