Question
QUESTION: Jeff this is the craziest thing I have ever seen. I have 4 zones on my system and draw water from a river. My second zone  will start right after the first but after a few minutes it will lose pressure and stop (pump still running). I cleaned up  the diaphragm and same thing. Now here is where the crazy part begins  - I took diagram and cut out 75 percent of the middle and replaced it. I started the timer and advanced to zone 2  everything seemed fine but sure enough it lost pressure and would only trickle out of the heads.  Now even more crazy results Zone 2 works fine when any other zone is running......  
Ok here are a few details in case you need them - I have a flowtech 2 hp pump that I just rebuilt.  I pull water from a river which is 40 feet below the highest sprinkler head  the  pump is about half way in the system and has worked fine for the last 4 years.  One thing I have noticed is that the pump output is 2" but about the last 8 or so feet in the elevation it is reduced to one inch - I have thought of increasing that to 1.25 or 1.5 but I am certain there is a reason for the reduction and have not messed with that. HELP   Eddy

ANSWER: If only zone 2 is not working, and all the other ones work fine, then I would suspect that the valve has a defect in it and probably needs to be replaced.

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QUESTION: What stumps me on this is that it works fine when another zone is running at the same time   I run 2 and 3 at the same time and it works - but with some loss of pressure I know I will get some dry areas....

Answer
My guess is still that it has something to do with the valve.  However, if you can use a multimeter, check the output from your controller on valve station 2 and make sure that it is 24 volts through the duration of the run cycle.  If the output is OK, then it really has to be the valve.