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The two peristaltic pump heads are on the same axle, so as one spins, the other spins the same amount. What tends to be a problem is friction with the water in the pipe, varying heights, or a few other things that can ever so slightly reduce the efficiency of one of the pump heads versus the other. The most important thing is that however you set it up, it will consistently be the same amount off.
To remedy this, you will find that slightly elevating or lowering the salinity of the water in your storage container will compensate for this. The pump doesn't have to be perfect, it just has to be consistent. The dual head stenner is extremely consistent. Over the course of maybe two months, your salinity might move up or down one ppm, but that can't be attributed to the pump. The skimmer is taking out water, your arms are dripping water out, bagging up corals, etc.