My sprinkler system on occassion skips zones. I once read that this can
be due to the fact that the pump needs to prime or is not primed well
and the water surges causing the zones to prematurely change. When my
pump first starts, it does take a good 3 min or so before water
actually starts through the main line. The well is about 20' deep. The
pump is about 10 years old but has always behaved this way - as far as
I can remember.
There is a check valve from the pump going to the well.
My system is mechanical. That is, the zones are changed using an
indexing valve that is rotated by water pressure.