They way the back compartments are designed if the water level is low it will show in those last two chambers even though the water level will look virtually unaffected in the display tank. If the last two chambers are low you just need to top it up with more water. Also the water levels in your chambers will drop daily so you need to top it up with RO water once or twice a week depending on the evaporation.
Its not an issue with the flow from your skimmer, I also thought that was the problem but the solution is far more simpler. Just top up