Low suction in shallow end skimmer

Are your skimmers on the same line (same valve/pipe going into the pump?) That is the setup I have where there is a line that goes from the shallow end skimmer with a tee for the deep end skimmer then to the pump. With everything equal almost all the water comes from the closer skimmer (deep end). However in bottom of that skimmer under the basket there is a small plastic circle i can move so it blocks more or less of the opening at the bottom to adjust how much comes from each skimmer by closing off some of the flow from the deep end skimmer. Every spring it takes a bit of tweaking to get it right since it gets moved out of the way during winterizing.
 
Have you looked at the slide valve in the bottom of the skimmer? Most have a little cover that slides back and forth to change the suction level.

Second would be, do you know how the piping is run? Are all skimmers/drains home run back to the equipment pad or are they daisy chained on the same pipe? If they are all on one pipe, this is where those little valves on the bottom of the skimmer come into play so you can adjust the flow.

A third possibility is that something fell down that pipe when the skimmer basket was out. One of my skimmer pipes had a large rock (egg sized river rock) down the pipe. I could see it down at the bottom, apparently (lucky for me) it was too large to make the turn in the pipe so with a bent coat hanger I was able to get it out.
 
Every now and then a leaf or debris will get in my farside skimmer and slow the flow. I turn my pump up, turn the valve to all skimmers and put my hand over the nearside skimmer hole to force all the suction through the farside skimmer. Been good for me so far. Luckily I haven't had any rocks in mine!
 
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