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I would do what I call due diligence troubleshooting. Loosen, remove then reinsert wire then tighten for all connections in the wiring path from the pulse sensor to the controller input including the input terminal. Fill any wire nuts with dielectric grease and cover any other terminals with the dielectric grease also. Micro corrosion or loose connections can cause the controller to miss a few pulses that you cannot see, in fact I have seen indicator lights on sensors work when there isn't a strong enough signal to the controller input terminal.
If you redo all connections that possibility is eliminated.
If you are running a test wash with no vehicle in the tunnel the laguna will automatically say failure. If not the case then either contact laguna or your local service.