Ok, I've found over the years that whatever the homeowner tells me is almost always not correct.
So I'm running with the idea that zone 12 has nothing to do with it.
Look to see if the guy didn't turn the shut off valve back on all the way after he installed zone 12. Is the shut off very old? Maybe it broke. Also check the water meter to make sure it's on all the way.
Also look for a pressure regulator that may have broke causing low pressure in all the valves.
You were right about some things... and I'm still looking for the solution...
Here's what I found out today (with the help of a licensed irrigation professional):
Zone 12 WAS wired as a separate zone. That wire was the master valve wire. That is because my house has the ability to switch from city water to well water for the irrigation system.
When we use well water, then the pressure is lower and we do not need the master valve because the line is constantly charged with water.
When we use city water, then we have to have the master valve, which means that when we are on city water that zone 12 cannot be separated and it must be tied to zone 1 (zone 1 and zone 12 are right next to each other).
We switched back to city water and found that we have water and the correct pressure in all zones (the well water will have to be fixed another day).
HOWEVER, zone 1 still lacks (even on city water) enough pressure to spray water more than about 5 feet.
The strange thing is that zone 1 has the correct pressure when the master valve is turned on and we turn on zone 1 manually using the bleeder valve.
Thanks for your patience!