It is very possioble that this mite have an effect. but wether or not, GET A BACKFLOW ON THERE QUICk! I definatly wouldnt leave it without backflow prevention. Its possible that the system is sucking in air........i would install a backflow and see if it helps, and regardless if it did or didnt it should be on there anyway.
Thanks
Ray
Rays Above and Beyond Automatic Lawn Sprinklers