I am measuring the output of two pressure sensors (0-5V output divided down to ~ 0 - 1V using 2k/10k resistor divider) using ADC3 through the primary ADC and ADC4 through the auxiliary ADC, both in SE mode referenced to ADC5. Both ADCs are referenced to a 2.048V precision external reference, with the high reference bit set. I notice I get significantly different results from the two converters. With an input voltage of ~550 mV on ADC3 and ADC4 the output code for the primary ADC is ~6845000, and for the auxiliary ADC ~11698000. Why are these so different?
Here is a code snippet for the ADC set up and conversion: