Maybe your pump needs to be slowed down alittle. Does your syphon have an air tube on it? When I built my auto syphons, mine have small tygon tubing that acts as a syphon breaker and I had the same issues so I slowed down my pump by installing ball valves in my system between the pump and where it dumps into my growbed. I can shut the ball valve to control my flow into my growbed. You can also control your flow with the piping downstream of you syphon. On the very end of mine I put a 45 degree pvc fitting that is not glued so therefore I can rotate it to help it start etc I also attached a small plastic pill bottle at the end of my syphon tube. I'm not sure if I explained it well enough. I hope this helps you with your syphon. There are some guys on this site that build and sell syphons that could probably explain this better.
You can also try at the bottom of the drain pipe a 45 reducing elbow that goes from say 3/4 to 1 inch and then a length of 1 inch tube running horizontally. This step up in size will allow air to enter from the drain pipe when the flow reduces breaking the siphon. This is the way I do my siphon drains and it works for me.
I would look at the hole you put in the bell to break the siphon.As I'm sure you have noticed the siphon starts over a period of a few seconds. Your hole in the bell seems to let only enough air in to reduce the siphon. It is working just enough to keep the bed from refilling. I've been there, done that, and got the T-shirt. Auto-siphon are tricky, I have four and each one seems a little different. I would recommend you notch the bell up to where you want it stop at. And make the tops of the notches as level as possible and of equal heights.
I would agree with Randy. If you're only using one hole to break your siphon, you might need a better airbrake. You could notch it or drill multiple holes at the exact same level around the circumference of the bell.
Or, you could do what Glenn Martinez does and put the notches in the top of your standpipe, then cut your bell off at the level where you want to break the water so your bell rests right on top of your standpipe to give you a nice, clean, level airbrake all the way around the base.....
Yeah, you can't drill multiple holes at varied levels; your holes need to be level with each other.
This moving 'cup' seems like a nifty addition to the snorkel.