I haven't received any other reports of lockouts in either of these areas.
1. There are 5 exits in the entry hall. After checking all 5 (4 doors and the stairs), Helen will be attacked and the plot will continue.
2. I'm having trouble understanding #2, sorry. After the Armour is defeated, Helen is able to access the southwest door, and an item there allows for access to the eastern door afterwards and the next fight.
It sounds like something may not have initialized correctly, which is extremely rare but can happen on very slow computers (a couple of people had issues like this back in MERCANOID that I could not replicate).