Don't know if you are still seeking suggestions or not, but, you might want to check the common wire. It usually is the white one in color and is sometimes the culpirt. I have seen that one connection can be bad and cause a "daisy chain effect". Check all connections to the valves in question and maybe even redo the connection. Make sure you use good waterproof connectors.
As for the timer / controller, what make and model is it? Have you done a full reset on the controller?
Did I miss something? What work did you do on the PVC pipe. I saw no mentioning of it in your post, and yes, it could also be the problem.
Josh
Irrigation /Landscape Lighting / Pump and Well Specialist