How long are the syphons, roughly speaking in terms of feet of pipe?
40% is a pretty good difference, that represents almost 2x as much driving force to overcome the additional line loss at the higher flow. Are the flows all different over this +/- 40% range or are 4 at one flow and 1 at the lower flow (I assume the former since you'd likely have mentioned such an obvious clue)?
What range of velocities do you estimate? That should give someone here an idea if air pockets are a potential factor or if they would be swept out once the syphon establishes itself. Personally, I doubt an air pocket would last.
The depth of the syphon below the water surface theoretically does not affect its capacity, that is set by the height difference between the lake and the receiving body. But, if one inlet (or several) was higher, it could be vortexing and drawing in air which would reduce its capacity, is there any sign of that?
I'd suspect some sort of restriction on the inlet side. Or if that doesn't work, something has been sucked and and jammed within the syphon.