I figured it out. The Sleep settings under Advanced Power settings were set to Hibernate after 180 minutes. I checked my other laptop and it was set to Never. I did not check this first because I didn't even know it was there. This explains why the Apps are all still open after waking the machine up (which would not be the case if the machine had been shutting down overnight). Anyway, problem solved.
My new 9560 exhibits inconsistent behavior upon lid opening. I have it configured to sleep when the lid is closed so I assume that is what it does. The computer should awaken immediately on opening and present the login screen and that is what happens when it has been left for short periods. However, when left for longer periods like overnight, the system appears to restart when the lid is opened. I don't know if it's coming out of hibernation or rebooting but it isn't simply waking up from the sleep state like it does after being left for a short period of time. Sometimes nothing happens when the lid is opened and I have to press the power button. Any thoughts on why this is happening? The system appears to be losing sleep status after being left for longer periods. Could this be a symptom of a hardware issue? It does this whether it's on charge or not.
Inconsistency on lid opening 9560