analog circuit: arduino nano 328 vs arduino mega

Dear all,

I am interfacing an PCB heart rate circuit with a arduino nano 328, then plot the graph using a simple pc app.

The input is analog, maximum 5V, and sampling rate is 100Hz

The circuit can be found here:

There is a one interesting observation: when using the nano , the peak of the heart rate waveform (amplitude) is extremely small, but when using the mega . the peak of the heart rate waveform (anplitude) is much bigger.

Can you tell me what are the differences between the nano and mega that may potentially cause the problems?

The author states,
"I have named the board 'Easy Pulse' and its output is a digital pulse which is synchronous with the heart beat.
"An LED connected to the output of the second stage of signal conditioning will blink when a heart beat is detected. The final stage of the instrumentation constitutes a simple non-inverting buffer to lower the output impedance. This is helpful if an ADC channel of a microcontroller is used to read the amplified PPG signal."

So, there's nothing to be had from it, analog-wise. If you digitalRead an "Analog Pin", if you must use one, do you get an unacceptable result that way?
Should this be utilised better with as a hardware interrupt (RISING, FALLING)?

Are you picking signals off of the LPF (not available on interface header)?