Sprinkler skips zones

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.
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