Craig - I got your voice mail la
1. Until the new planting, zone 3 worked. After the planting it did not.
2. You saw wire scraping.
Well Watson, there appeared to be no damage on the wire, yet there is short circuit.
Hmmm, lets look at the wiring. Electricity , and the bumper cars that the electrons play are really small. I mean it. Very, very little. Can't see 'em. The normal gauge for sprinkler multi-wire is 18 gauge.
18 gauge (a little bigger than phone size) is pretty small, and difficult to visually evaluate. But not as small as electricity.So maybe something is going on that we can't see with our eyes?
The red and blue wire are exposed. What color is the common wire in the controller, is it red or blue? Electrical code states that it is white, but hey this Florida. "We don't need no stinkin' codes"!
If so, there could be a very tiny nick, bleeding electrons through the soil (moisture is a conductive) that is shorting the controller. If the common is white, it could be nicked also. What color wire is attached to zone 3 (bad zone), red or blue?
First, read this post about replace sprinkler controller. It will save me a lot of typing.
Second, dig up the wires in front of the exiting conduit. Try to have 12'' at least of slack above ground, and cut the entire bundle. Now attach a 7-18, seven strand multi-wire (might as well as have a spare for all this work), attach it with tape (or however you want to do it) and pull the new wire into the building.
So now we have new wire to the controller (even though it is not the problem) and at least 12" out of the ground of the old wire. Now we make a junction box. The 12' of slack allows someone to easily check future wiring problems because the wires are easily accessible. Do not connect the old wire to the new.
So why go to all this trouble if the scrape is 3 feet away? It wouldn't matter is the scrape (bleed/short) was two inches away. We need slack wire to make proper connections.
NOW, we fix the problem! Where the wire was scraped, dig two feet electrically downstream (away from the controller). Now cut the bundle at the "red and blue" wire scrape. Put in a junction box, and leave enough wire in the box so that you can pull it out for testing (see valve repair video at diy sprinkler system troubleshooting ).
Pull new wire from the junction box at the controller to the "red and blue wire" junction box. Connect all the wires using silicone wire nuts.
In conclusion, you have two functional junction boxes by-passing the wire scrape.
This is not to say that you can't take an easier route by using some old speaker wire and black electrical tape and make a connection that works,
But you'll need someone else's blog for that advice :)