RE: Two stations running together
It does appear your problem maybe in the wiring with the valves.
Allot of contractors will use the same color of wire at the controller for a zone as they do for the valve.
So what I would do is go back to the controller and see what color of wire they used for zone 3 and 5 and then
start opening valve boxes until I find the valves that are wired with the same color of wire and see if they wired
the zones together. If they didn't use the same colored wires, you can figure out what valves are zone 3 and 5 by simply manually turning the valves on at the valve boxes, then check to see if they are wired together.