Because I'm not exactly sure how your system is set up, I'm just going to describe my growbed's siphon and drainage system.
In the growbed, the siphon has a Media Guard made of a 4" diameter PVC pipe with 1/2" holes at 1" intervals. The Media Guard is higher than the gravel level. This keeps the gravel from clogging the holes in the siphon's Bell.
Inside the Media Guard is the siphon's Bell, made of a 3" diameter PVC pipe with 1" holes at the very bottom and a "knock out" cap at the top. The reason for the knock out cap is because a regular cap was too big to fit inside the Media Guard. The fit between the pipe and cap that makes the Bell needs to be airtight, and I had to apply aquarium silicone to the top of the bell to achieve that. The top of the Bell is somewhere between 1" to 2" below the gravel level.
The Siphon Stand Drain consists of a 2" pipe going into a 2"-to-3/4" reducer fitting going into a 3/4" elbow that attaches to the bulkhead fitting on the growbed wall. The bulkhead is mounted about 1" from the bottom of the growbed. The top of the Siphon Stand Drain is about 1" below the Bell's cap. There is a small hole (3/32") drilled into the 3/4" elbow to allow for a constant trickle of water out of the growbed; if the pump fails, the growbed will slowly drain instead of having standing water that will drown the plants' roots.
On the outside of the growbed, the bulkhead goes to a 3/4", 45* elbow that points downward (please note: I'm using * for "degree" because I don't know where the degree symbol is on my keyboard). The 45* elbow connects to a 3/4" tee fitting. One side of the tee is the Return Pipe that goes back to my Sump Tank. The return is a 3/4" pipe connected to a 3/4" elbow (pointing down) connected to 3/4", 45* elbow that empties into the Sump Tank.
The other side of the tee is connected to a 3/4" elbow (pointing up) with a 3/4" pipe that rises above the growbed. I call this the Burp Pipe because it "burps" when the siphon breaks. When the siphon in the growbed pulls air into the Return Pipe, the Burp Pipe also pulls air into the Return Pipe helping to break the siphon effect. At least, that's my theory as to why it works.
Just for the sake of clarity, all elbow fittings that were not described as 45* are 90*.
Sorry I don't have pictures; I haven't taken any yet. And I would put up a Google Sketchup drawing, but I'm typing this in the few minutes I have before I have to go to work.
Hope this helps.
PS. Forgot to mention that I'm using Red Lava landscape rocks as my gravel. It's my understanding that gravel that is too small will cause drainage problems.
(please note: I'm using * for "degree" because I don't know where the degree symbol is on my keyboard)
The degree symbol (º) can be inserted by holding the Alt key and entering 0186 on the keypad.
Have you thought about adding a vent pipe to your siphon? I have mine vented and it has worked without a problem.
A basic plumbing practice is to always have air behind water. It works for sinks and siphons!