Some sort of isolation from the general Vcc must be provided to the reference input of the ADC. A small series resistor might be of help, i.e. a 50-ohm or thereabouts value with a capacitor to GND at both ends, so high-frequency, high-energy spikes, particularly as caused by your stepper driver won't pollute your reference voltage.

You should also consult the datasheet to see how much unadjusted error there is in the general case. IIRC, it is on the order of 1 lsb under utterly perfect conditions.

In your place, I would put a very well regulated well-controlled (within 1 mV) input into the reference, and another well controlled input into the ADC input just to see how well it interprets the input. You should, without too much trouble be able to obtain a consistent reading to that 1 LSB random error. If you're not, you should make a thorough examination of your reference generation and bypass scheme.

RE