" zone 3 and 4 come on at the same time and both run through the zone 3-4 run times"
Disconnect the wire from zone 4. Turn on zone 3. Do they both come on?
Reverse procedure.
If they both come on under either condition, or if either refuses to come on under either condition, you have a wiring problem. Or...
The low pressure does sound like either a leak, a pinched line or you cross-tied two zones. Maybe 3 and 4 were accidentally tied together, which would explain why they both come on and have low pressure.
Don't know why they keep running through the program.