When you top up the dry fertilizer in the fert bin, you end up with a fine dust layer between what was left in the bin, and the added fertilizer. When the bin empties to this level, the dust will set off the alarms. If you get out an check the system, you won't see anything wrong. But, if you run it for a few minutes until the layer of dust disperses, the alarms will go off.
Depending on the type of alarm that is occurring, there may be different reasons. If it is a CLN message, the fertilizer dust my be causing a bit of a build-up in the sensor. If is is a HI RATE message, the sensor is counting more particles/second of "dusty" fertilizer than the normal fertilizer. This is expected as the "dusty" fertilizer has more particles/lb than the normal fertilizer.