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. 
NOTE: When reinstalling the meter cover make sure you put it back on right. There is a "dimple" near the center cable connection that should be pointing towards the outlet side of your valve. This is to the left if you are standing in front of the valve.