Question
I turned on the water to my sprinkler system this past week. My controller (Hunter ICC, 14 zones all Hunter equipment)was off and to my surprise the system started to water. I unplugged the controller, took out back-up battery and the system was still on. I had to shut it off by turning off the water.
The system started to cycle through one of the programs I had. Now when I turn on the water only two zones work.
I re-setted the controller several times. The system is still not responding to the controller. The only time the system goes on is when I turn on the water and only two zones work.  

Answer
Very perplexing.  Controllers do go bad, and when they do, strange things can happen.  However, if you disconnected the controller, the system should have shut down.  Try unplugging the controller, remove the battery, leave it off for about 5 minutes.  Then plug it back in, then put in the battery.  See if this works.  If not, you may have to replace the controller.