Sounds like your ATK is running past the programmed “max time on” and shutting off as a precaution. If standalone, this should learn over time. If connected to an Apex, you need to adjust the programming of the auto top off. “When On > 003:00 Then OFF” is my ATO code. If the pump runs for more than 3 mins, it shuts off and raises an alarm.
As I recall, the alarm will be triggered if the upper sensor is under water for > 10 minutes, if the pump runs more than twice as long as the average fill time from the last 5 fills (IQ fill) or if it runs for more than 5 minutes.
The problem with the ATK is that when used in stand alone mode, these alarms settings are more often problematic than helpful, and once an alarm has triggered, you have to power cycle the device to reset it. (Resetting it also resets the IQ fill memory, too, so the design significantly limits the usefulness of that feature.) The feed mode on my return pump turns it off for 30 minutes, also letting the level in my sump rise. That would then trigger the high water alarm, so I would have to come back and reset my ATK every time I fed my fish. Ditto if you use a sensor in your ATO reservoir and it runs dry. Instead of simply turning on again when you fill it, you have to reset the entire device.
Kalk also causes issues with the anti siphon valve and the float valve by clogging them with buildup. I can't necessarily blame Neptune for this, as it's a problem intrinsic to kalkwasser, but they should be clear about it in their instructions.