sirDragonHeart:
On further testing with the non-functioning modules, I saw that the flags for the interrupts get set (A1F and A2F correspondingly) in the status register but the INT pin does not go low hence the arduino does not see an interrupt.
Was the INTCN, A1IE & A2IE bits also set in the control register (0x0E) to enable the Alarm match to also trigger the interrupt?
Also I think BBSQW needs setting to 1 to enable square wave output when battery powered.