The 18MHz are not the sample frequency, but the ADC clock. To see if all settings are made correctly, consider to post your complete project. To do so, use
Creator->File->Create Workspace Bundle (minimal)
and attach the resulting file.
A cause might be that a higher ADC clock will draw remarkably more supply current which can influence the voltage delivered by the battery.
What do the readings look like for both channels ? How much variation
do you see ?
ADC settings are as follow:
Channel sample rate 3676sps, Vref select: Internal 1.024 volts, Single ended negative input Vref, so the sample range is 0.0 to 2.048V.
One channel is for battery voltage detection, the battery's voltage is 3.798v, I use two resistor 330KOhm and 200KOhm to make sure input voltage is below 2.048v. I measured the input sense voltage is 3.798v*200/(330+200) = 1.412v, but the ADC sample value is 2672. 2672/4096 * 2.048 = 1.336v.
Another channel is for circuit current measurement. ADC channel sense voltage is 175mv, and ADC sample value is 340, this 1:2 is match my circuit, and I think 5mv tolerance is acceptable.
Keep in mind unless you have buffered the ADC inputs the ADC has a
finite input Z of ~ 2.2K ohms, so that will affect your V divider design
values and Rsense value for the current measurement.