I was having the same "no timers" problem AND wanted Notification Center sticky notifications that I've seen on many messages in these threads. I've got timer working exactly the way I want now and it's freaking awesome. I'm using El Cap and here's what I did:
To get the "Current Timer" functionality to work I ran "timer nuke" to reset everything, then created an ALARM. Once I created the alarm, everything shows up as it should when looking at the timers. Dunnow why, but nothing showed up until the alarm existed.
To get Notification Center sticky notifications (no Growl), go to System Preferences -> Notifications and look for Alfred. Set Alfred's alerts to "Banner". In the same window look for EggTimer and set it's behavior to "Alerts". Now when I create a timer or alarm I get a notification that goes away after a few seconds, but when a timer goes off it stays there until I click "Close". Perfect!
Hope this helps someone and thanks Carl for a killer tool!