As a follow up - when I run each zone manually they seem to operate Ok. Only when running via timer do they run at less than full pressure

Do you mean by manual that you are turning on the valves using the bleeder screws? Is this a well for irrigation only?

If you are using the manual mode on the clock and it only has low pressure when running on the timed program and your well also it supplies water to the house, it could be a water usage issue. If it is set for the time when the water in the house is being used such things as showers, laundry, ect, that could explain the low pressure.