I got pretty much this Problem from the FAQ:
phpPgAdmin ask me to re-enter login information for every page I access!
However, it works just fine when I only load the main frame and I can browse the Database. If I load the full frameset, every click requires reauthentication.
So it does not look like a session problem, but I checked that just in case and both frames have access to the session cookies and the session cookies correspond to session files in /var/lib/php5.