without knowing what algorithm your SOC meter uses I can't say whether jumping around is a problem or not. if it is analog, it is a specially calibrated voltmeter, nothing more. If it is digital, it could be the same, or it could be going so far as to be counting KwH and be taking into account rate of discharge, temperature and battery type in computing SOC, depending on how fancy it is.
Sediment shorting out cells is unlikely to be an issue that comes and goes, and is unlikely unless your batteries are old (or damaged) or perhaps a cheapo brand.
I am not aware of any SOC meters that talk directly to the controller but that does not mean that they don't exist.
Knowing model number of controller, SOC meter, and manufacturer/model of battery etc might allow for more than just general suggestions from the group.
Good Luck.