Mike, if I understand it correctly, it doesn't go into siphon mode until ALL pipes, inlets, vents, etc are under water. Can you take a pic of your upper setup. Its hard some times to grasp everyones different lingo for items and such.
If you take a look at that link I posted, it shows the vent just under the height of the spillway. This could be your problem, easily fixed if it is.
