You may have to replace the controller but try this first.
Unplug the controller. Take out the lithium battery. Let it sit for a few minutes. See if this doesn't reset the brain.
Make sure the transformer wires are correctly hooked up to the controller.
Double check the fuse. You might have two bad fuses. There's a good chance that's the problem.
Any 6 station controller will do. You can't go wrong with the Hunter Pro-C.
www.sprinklerwarehouse.com/Sprinkler-Timers-Controllers-s/23.htm