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А Вы это читали?
Scanning Multiple Channels
Since change of analog channel always is delayed until a conversion is finished, the Free Run Mode can be used to scan
multiple channels without interrupting the converter. Typically, the ADC Conversion Complete interrupt will be used to per-form
the channel shift. However, the user should take the following fact into consideration:
The interrupt triggers once the result is ready to be read. In Free Run Mode, the next conversion will start immediately
when the interrupt triggers. If ADMUX is changed after the interrupt triggers, the next conversion has already started, and
the old setting is used.
Может, поступить как они написали, и выбор канала делать в прерывании от АЦП, а не поллить, как Вы сейчас делаете?
Кстати, может, "враки" АЦП по конкретному каналу - это значение из другого канала?
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