Thanks J-M-L! I tried using the 3.3v on the AREF pin and the values on the Arduino Uno now came close to those on ArduLog indeed.
Do you have any idea why the z-value is either 256 or 512 when I use the RTC sketch as attached in my original post? It is suspicious I get 1/2 and 1/4 of the 1024 values, suggesting I'm only reading 1.65 or 0.825V, but the results from a simple analogRead script suggests this is not a hardware issue.