I just came up on this thread and read a good bit of it.
One thing about siphons is that they pretty much never trickle at partial flow, they would lose the siphon if they did, they are at full flow or empty. like you said they are doing now.
I would guess you may have had a restriction, could have been an animal or turtle sucked into your siphon inlet and more then likely got caught in an elbow or 45 degree fitting where your 6" pipe turns to level off going across the top of the dam.
It may have rotted away or got washed on out since then which would explain why its working now.
if it happens again I would seriously consider hiring someone with a sewer camera, or maybe you could rig a scenario up with the gopro, to investigate the entire length of the pipe, I am almost positive you had a restriction. a 45degree fitting is notorious for stopping something that would otherwise slide right thru a straight piece of pipe but wont be able to navigate the elbow.
Good Luck!