I'm definitely not a 'bean animal' expert (or reef tank generally) but, I did drill my cube tank and put a bean animal in it so, I have some experience. It seems like you have a fundamental problem with your full siphon line. As I'm sure you know, the 'full siphon' is supposed to carry the vast majority of the water down to your sump. The open line is supposed to carry a tiny amount, while the emergency is just that, it stays dry absent a failure.
If you have a bunch of water coming down your open line with the full siphon gate valve fully open, you probably have one of three problems:
1) your return pump is pushing more water into the tank than your full siphon can handle (this is not normally a problem as far as I know); in this situation, your full siphon will be 'working' but, it will simply be unable to handle the flow;
2) where your full siphon line enters your sump, the pipe is too far down in the water; in order for the full siphon to 'form', the piping needs to purge itself of air; if the pipe is too far down into the water in the sump, the purging becomes more difficult because the air needs to be 'pushed' down through the water in the sump to clear the line; or
3) your pulling air into your full siphon line in the overflow box. In this case, your full siphon line is capable of purging itself of air at the bottom but, you're adding air back into the line at the top, breaking the full siphon (or not allowing it to form).
Note, it is also possible to have your full siphon gate valve open so far that a full siphon doesn't form depending on return pump flow but, this should send all water down your full siphon line, with the problem being noise from the gurgling due to the absence of the full siphon.
Based on the picture of your overflow box and the fact that the water is going up and down in the box, I think you likely have problem #3 above. Your full siphon line looks only marginally lower than the open line in the box and very high in the box generally. I think your full siphon is pulling air at the top, reducing flow, causing the box to fill higher. At this point, your full siphon line stops pulling air because of the higher water level in the box and a 'full siphon' actually forms. Now the capacity of the full siphon line greatly increases, pulling the water water inside the box down. As the water goes down, the full siphon line starts pulling air again, breaking the siphon, reducing the line's capacity and starting the process over again.
My suggested effort at a solution would be to take the elbows off your full siphon line inside your box (and probably on your open line as well) and put your full siphon line as low in the overflow box as possible to reduce the possibility of a vortex pulling air into the line.
If you're going to keep the elbows on your open line, I think you may need to drill a hole in the top and possibly add some airline tubing, like a durso.
FWIW, all three lines in my overflow are just open pipe lines. One benefit is that this allows me to see exactly what is happening with each line. One possible disadvantage is, with no strainer, there is some risk I suppose that some critter will find its way into a line and clog it.
I hope this all makes sense. Good luck.
Matt
