Hi,
A look at the datasheet shows A.2 is a schmitt trigger input ... not so good for such measurements.
Measurement differences with other ports come from here ...
The only way to keep your board as-is would be to raise the voltage from your trafo ... the trigger levels occur on the "very low" ( read closest to zero crossing) part of the sine.
no real hope of saving your board ...
Alain
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Why insist on using 32 Bits when you're not even able to deal with the first 8 ones ??? ehhhhhh ...
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IF there is the word "Problem" in your question ...
certainly the answer is " RTFM " or " RTFDataSheet " !!!
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