Have you replaced the GFCI, to ensure it's not failing?
The only other thing I can think of is there aren't enought minerals in the water to allow it to pass much of a current, so there isn't enough to trip the GFCI until the level is 100%. Or you are getting a capacitor action that discharges and trips it.
But a GFCI should trip at the slightest imbalance in the poles...but it's 12v right?.......
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