Rainwater stratification in my saltwater pool?

I have a new-to-me 11000 gal in-ground pool with a Aqua Rite SWG system, my first experience with these devices.

Now that the weather is cold, I have the pump set to run three times/day about an hour each time. We've had quite a bit of rain lately and I have added some salt from time to time to keep the salt level in the proper operating range.

Several times, after a rain, I've noticed the "low salt" light and "check cell" lights on in spite of not being low on salt. When this happens, the salt reading is below 1000, sometimes as low as 250ppm. As far as I can tell, the unit shuts down when it detects low salt and remains off until it is reset.

After forcing the pump to run for a couple of hours and resetting the Aqua Rite system, it registers a normal salt level which I am able to verify with my salt testing kit. This level varies to some degree depending on how recently I've replenished the salt as required since each time it rains, the pool water is diluted a little bit. No surprise there. However, I keep the salt level in the range recommended by Aqua Rite and I cross check the panel reading against my chemical salt testing kit.

I wonder if when it rains with the pump off, the lighter fresh water stratifies on top of the heavier salt water such that when the pump kicks it initially sucks mainly rain water via the skimmers. Could the the SWG be detecting this nearly pure fresh water when it starts up (along with the pump), causing a low-salt shut-down before the pump has a chance to mix the recent rain water in with the rest of the pool water?

I called Aqua Rite and asked this question, but all the "expert" could tell me is that rain water dilutes the salt water. Duh..... I think I could figure that out on my own.

He also said the Aqua Rite unit will not begin measuring the salt level nor will it start generating until it runs for at least an hour and a half. He claimed it is impossible for the unit to be reacting as I suspect it does. I thanked him and hung up since what he said didn't make any sense. When I turn the unit on and look at the voltage and amperage at the cell as well as the other readings, it takes less than a minute to start reading the instantaneous salt level and begin generating.

Within a minute of starting, the control panel shows the generating light on, and all the parameters appear normal. Where did this guy get the idea that it has to run for 90 minutes before it starts measuring the salt level and generating chlorine? He didn't seem to be the sharpest knife in the drawer, so I didn't argue with him.

Anyhow, has anyone else experienced a temporary shut down and low salt warning after starting the pump following a period of significant rain while the pump is off?

Now that the rain has stopped, the system is operating quite normally.