Hi - which way round is the discrepancy (pulse count reading > CT or vice versa)? If the cumulative CT is reading higher might it be due to an issue similar to the one I had here: Positive offset on both solar production & home consumption - #23 by Robert.Wall
Even a smallish positive offset on your CT will lead to a meaningful cumulative drift e.g. if you consistently read 10W over the real value that will give 0.24kWh per day.