PortletPreferences are user specific otherwise it's not really a preference. ;-) I think what you are seeing is probably related to session clean up when user logs out. This should be fixed in upcoming GateIn 3.2.GA.
To verify this assertion, can you please use different browser when you login as user2?
Thanks, Prabhat! I thought I was going crazy there for a while.
I had user2 pick blue, then logged in as user2 in a different browser and, voila!, the background was blue. So as expected, preferences are unique to each user.