OP, as others have noted, you have your Gyre hooked up to the B port, which is why A turns off after you saved the settings; the controller tries to run your program but finds that the A pump is missing and therefore turns off.
Both sides of a Gyre run at the same speed, since they're on the same motor. If you want it to run at a randomly varying speed, you can use random mode. Enter setup. Select the correct pump A or B with the wheel, and set with the center button. Now select the random mode with the wheel; turning the wheel clockwise, the mode order is constant, pulsing, gradual pulsing, random, and alternating. Select random (large/small/large arrows), and set. Then use the wheel to enter the maximum percentage speed, and set. With other modes, you can set several variables, but with random, all you can set is the maximum. Exit setup and that should do it.
Alternating mode is only useful if you have two Gyres and/or have switched one of the impellers on your one Gyre so that it can pump in both directions.