The "meter cover" 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?