The battery detection is done by the motor encoder, not the amplifier. If there is a break in the cable or if the encoder is bad, you could get a battery alarm on just 1 axis.
Before swapping anything out, I suggest removing the feedback cable from the motor and measure the battery signal. If you have a 15-pin D type connector (used with smaller alpha motors), measure between pin 14 (6V) and pin 10 ( 0V). If you have the larger alpha motors with the 19-pin feedback connector, measure between pin R (6V) and pin S (0V).
If you actually have the alpha-i motors (not the alpha), that use the 10-pin feedback, let me know and I'll look it up.