Excellent obvservation and one that is often missed. Most softener meters are not highly accurate especially at lower flow rates. This is due to cost and space design considerations. Your city water meter is highly accurate at even the lowest flow since they are charging you for the water. The design of these meters is based on positive displacement (not sure of the technical term but you get the point). Softener meters are typically slip stream or turbine/impeller designs. Low flows do not get registered, but since most softeners have reserves built into them, this is usually not noticed, RO systems, humidifiers, faucet and toilet leaks are usually not registered. If the problem is particularly bad, you can compare the city meter to your softener meter to see the difference. Sounds like you got it perfectly though, you may have to adjust your system to accomodate the missed water.