RFID (13.56MHz) tag properties depending on read distance
The problem could be in your IC or with the card construction, and it looks like the tuning.  The return signal you are seeing is dependent on two components: quality factor and the resonant frequency, both resulting from your card's antenna and the input capacitance of the the device.  A higher &quot;Q&quot; will give you a better range, but only if the resonant frequency is close to the transmit frequency.  A lower Q will allow a wider variance of the resonant frequency at the cost of signal strength.  Since the IC's input capacitance varies from chip to chip, a trade-off is made to allow for some variance in the resonant frequency.
Although two coils may appear identical, they also may vary because the encapsulant is a dielectric and adds a capacitance component to the resonant frequency equation. So consistency of manufacture is at a premium if no testing is done on a card-by-card basis.  If the antennas are indeed identical, then the Q factor must be too high for the variance in input capacitance (and resonant frequency) of the device with that coil design.  This is not too likely, since there is so much published material on how to shape the antennas.
One other idea - there is an Android app available from NXP that can detect whether you are using an NXP device or a clone.  The clones are somewhat notorious for variation.
Good luck!