The "meter cover", part # 14038 can be the reason your Fleck Econominder is not regenerating automatically. Once you have determined the timer motor is functioning properly, the meter is the next part to check.
 1) Is the cable securely connected at the valve head side? This connection is inside the back of the timer control head.
 2) With the valve in By Pass or the water off, remove the meter cover. Four screws hold it in place. Note how it is installed so you can replace it the same way it came out. 
You need to check for debris or build up around the impeller, 
 part # 13509 ( looks like a paddle wheel ) in the meter body.
 3)With the cable disconnected from the meter cover, 
does the cable move the program wheel ( the dial on the front of your timer head ) freely by hand? 
 4) The way to test the meter cover portion, is to remove it. With the cable connected to the meter cover, turn the cable with your hand. You should be able to cause the white gears inside the meter cover to spin ( looking from the underside of the meter cover ) . They should continue to spin for a second after you stop twisting the cable by hand. If it is very very hard to move, or stops as soon as you stop applying pressure, then you need a new meter cover. 

The setting ( each digit equals 100 gallons ) on the 5600 meter determines how much water is used before regeneration is run. It does not regenerate every night, only as water usage dictates the need. To compute the proper setting of the program meter wheel ( dial on the front of control ), you must know your hardness ( & iron level, if any ). You also must know the capacity of your resin tank. The average size resin tank is 9" x 48" and holds one cubic foot of resin. Resin has a maximum capacity of 32,000 grains removal ( when regenerated with about 18 lbs. of salt ). Softeners should be sized and set to work at 75% capacity ( which requires half as much salt ). With the capacity and the hardness level known ( add 3 grains hardness for each ppm of iron present in the water ), you are ready to set your program wheel. Take the grains capacity of your resin tank times 75% ( 0.75 ) divided by hardness ( in grains ), then subtract 75 gallons per person using the water as a reserve.
Example: 32,000 grains x .75 = 24,000 divide by 20 grains hardness = 1,200 gallons - 150 ( 2 people ) = 1,050 setting.
You set the gallons by lifting the clear portion of the program wheel, and align the white dot with the number of gallons you wish the unit to use prior to initiating a regenerate ( the night following the meter reaching Zero ).
Also the salt setting should be 9 lbs. per cu. ft. of resins ( 32,000 grains ). You can find this adjustment on the "Brine Cam" gear inside the back of your control head. It is a small halve moon shaped piece that it held on to the Brine Cam with one screw. It has a small pointer which indicates the pounds of salt to be used per regeneration.

If you do not know your resin tank capacity, send us the tank's height and diameter, and we will let you know how much resin is normally used in your size tank. We will also do the rest of the math for you, if provide the hardness & iron levels ( note: most "city" water does not contain iron ). Also, you might need to know that 17.1 ppm of hardness = 1 grain of hardness.

Your water should feel soft and "slippery" all the time. Always remember you need very little soap when you have soft water.