Different voltages between arduino UNO and multimeter

Its the "around 2.5 Volts" that is of concern. Still a 0.07 volt disparity is excessive.

I would:

  1. Print out the raw A/D counts for both A0 and A1.
    Print them for more that a few seconds to see if the readings are stable.
    It would be best to use the IDE Serial Monitor if you can. (simple is best for troubleshooting)
  2. with your voltmeter measure the A0 and A1 voltage right at the board.
  3. Also measure with your voltmeter the 5V right at the board.
  4. Don't change the reference (for now).

These numbers should allow the error source to be found.