I have not seen or heard of this issue before. Are you creating the JSF
Libaries from the Preference page, or while during creation of a JSF
application? When you go back to "configuration" and you see "[missing]",
is this from the JSF Library Preference page? Does this occur in the
same session, or have you restarted your workspace?
When you say latest Eclipse and WTP, which build? What operating system
are you using?
Can you please enter a bugzilla report with steps to reproduce and a
screenshot?