You should convert ADU to e using the (inverse) gain in e/ADU for a real measure of S/N. This is probably what your software is not taking into account. The gain does not change the number of photons captured (assuming it’s not saturated ) .
You can quite easily measure the gain in the right units see here for example http://www.astrosurf.com/buil/isis/noise/result.htm
Regards Andrew