GW,
I'm no expert on siphons but I've been researching them for about a year now. My guess would be that your siphon is sucking air at some point. I think that is what the thumping sound is.
In one of your other posts you mentioned that one 90 degree elbow is attached only with screws (no solvent weld). Is that elbow completely submerged or is there a tiny whirlpool at the joint? Same deal with the submerged part of the vent pipe. Is there a whirlpool there? If so air is being sucked in. I'd also check vent piping joints and valve, any part that is now submerged.
I did a quick check
at this site on flow rates. Using 8" pipe, (3) 90 degree elbows, (2) 45 degree elbows, and 50 lineal feet of pipe with a 10 foot drop a siphon should exceed 2000 gpm.
