i had a similar problem. Ubuntu was left me log in in console with any password for superuser. Except when i connected with -h localhost in psql line command.
I Observed too that "localhost:8080/MyJSPSiteLogIn" - showed: Fatal: autentication error with user "user".
pg_hba.conf was ok.
I noted had two versions of postgres running in the same service.
Solved - uninstalling inutil version.