Is the sump end of your piping submerged? If not, you can get air introduced from the bottom, which will make the flow of the siphon fluctuate.
Give a little more info on how it's fluctuating though, as it could be the valve needs adjusting, or some other reason. The link below is very helpful in the meantime:
http://gmacreef.com/herbie-overflow-reef-tank-plumbing-method-basics/