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What is the exact effect to the analog section of the SAM when more than one channel is enabled, even if for short time only? Does this mean that the related analog input pins are then electrically connected with low impedance?
Looking at the logic diagram on the datasheet it seems that there is a multiplexer before the ADC, so theoretically only one pin at a time can be connected to the ADC.
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may you post some more information on your test setup? May the inaccuracy you're experiencing be due to high impedance on your analog source?