Good suggestion, but I am basing on these steps from the manual below. So, to me when the system is following the timer, it can add water to the brine tank 2 hours before the regeneration process. But I would think that with manual generation the first step is actually to add water to the brine tank and its not happening.....
So I don't know what could it be
Brine Tank Fill
The first step in preparation for the regeneration is to add water to the brine tank. The amount of salt the conditioner uses in its regeneration is directly related to the amount of water added to the brine tank. The salt will only dissolve into the water until it reaches a point of saturation, then no matter how much longer it sits, no additional salt will dissolve. Many softeners add a fixed amount of water to the brine tank at the end of each regeneration cycle. With that type of unit, the water sits in the tank until the next regeneration, usually for several days. Your EC4 uses a more sophisticated and efficient approach called "proportional brining." The computer continually monitors your water use and decides if regeneration is needed today. If regeneration is needed, the computer moves the valve to the brine refill position about two hours before the scheduled time of regeneration. You may hear the motor running and some water flowing at this time. Because the computer knows how much water you've used, it calculates the exact amount of salt that will be needed to completely restore the system capacity. Then it adds just enough water to the brine tank to dissolve that much salt. So you can say it creates brine in proportion to the amount of capacity you need to restore - it doesn't waste salt.
EXAMPLE:
If the time of regeneration is set for 2:00 AM, you may hear the system apparently start to regenerate at 11:45 PM. What it is actually doing is running the brine fill cycle. It will fill the brine tank for a few minutes, then return to its normal home position for 2 hours. The actual full regeneration cycle starts at 2:00 AM as scheduled.
Soak Cycle
After adding water to the brine tank, the valve returns to home position and waits for two hours. This gives the salt plenty of time to dissolve and ensures that an accurate salt dose is used. The system is still providing treated water to your home during this cycle.
Backwash Cycle
At the exact time of regeneration, the valve moves to its backwash position for the start of its actual regeneration cycle. In the backwash position, the normal flow through the pressure tank is reversed, with water flowing from the bottom up, so that the softening mineral is lifted and cleaned. This removes any dirt or particles that have accumulated on the top of the mineral bed. As is true of the entire regeneration cycle, all the water flowing through the tank at this point is sent directly to the drain. None of the regeneration water enters your supply pipes. If you use any water during regeneration, the system provides you with untreated water that completely bypasses the tank.
Brine Draw / Slow Rinse Cycle
After the system is backwashed for several minutes, the valve moves to the brine draw position. In this position, the valve creates a vacuum to pull the brine solution out of the brine tank. The brine solution flows slowly through the mineral bed, removing the hardness ions that are attached to the softening resin and sending them to the drain. After all the brine is drawn out of the brine tank, the system continues to slowly rinse the
MANUAL REGENERATION:
Although it may never be necessary, you always have the option to start an immediate regeneration using the "manual regeneration" key on the keypad. The manual regeneration will start with brine tank fill and a 2 hour soak cycle as described above. Since a manual regeneration is primarily intended to recover from unusual circumstances, such as allowing the brine tank to run out of salt, it is assumed that you need to recover full capacity. Therefore, a manual regeneration always uses the maximum salt dose for your size of unit.