Voltage reference sampled by ADC (12 bit) gives value that is off by more points than other measurements
Try providing a little more settling time (a few msec) before taking each measurement.  By this I mean time between when the ADC channel is selected and when the conversion starts.  I use the REF3020 and it has poor response to changes in load, even though it can provide high current into a fixed load.  You won't see it with a DMM or even a scope because it's hard to set the trigger set very fine.