I finally got it to work by going to preferences and turning off (unchecking) all apps from the notifications center, then turning them back on (checking the first box), then rebooting the mac.
I have left the Mail app on and now am getting flooded with notifications, both popups and in the notifications center.
We shall see if it also works when Mail is not running. That would be helpful in that I like to get notifications of incoming mail, but prefer to use the gmail browser client rather than Apple's Mail Center, which still lacks in spam filtering capabilities. Trying to figure out a way to get Gmail to not send filtered spam to the Mail client, but that may entail creating a new gmail account that would receive only the good stuff.