To correctly program the align ESCs you have to be using a model profile on your transmitter that has a linear throttle curve, 0,25,50,75,100. If not, the ESC won't be able to determine where your throttle stick is. After you initially get it programmed correctly, then you can change your throttle curve to what you intend to fly with.

Also, if you have a Futaba transmitter, you have to reverse your throttle channel to work with the align ESC.

If you want to enter programming mode, you should connect the battery to the ESC with the throttle stick in the highest position. If you have already programmed, you need to connect the battery to the ESC with the throttle stick in the lowest position to be able to fly.

If you plug in the ESC while the throttle stick is somewhere in the middle, it will just beep at you, until you return it to the bottom position.