I will totally concur with skimmate being a drain on salinity... The only way it would not contain salt would be if it was distilled
And since I doubt your skimmer(s) are pushing foam near the boiling point, the liquid in the cup has not been evaporated/condensed during the process and thus is most probably not pure water. So salinity is thus decreasing because top-off water is pure and diluting the tank.
Same applies if you are dripping new tankmates -- I always add to the tank about how much I plan to drip out of the tank prior to starting acclimation so that my ATO doesn't run extra and dilute my salinity (which as everyone I have set to a specific level on purpose)