I have created several queries named and saved them, but they don't show up in the Query window. Yet, if I go to the New Query window and click the tab to base a new query on an older query, the queries that don't show up in the Query window, do show up in the list to base my new query on.
can anyone tell me what is going on here, and how to fix it?

You've probably hidden them go to options /show hidden objects.
HTH