Thanks, i think its because of incorrect value of BATT_AMP_PERVLT, initially i tested with BATT_AMP_PERVLT=40.0 which is given by Matek, now when i contacted matek they told me to use
BATT_AMP_PERVLT=60.6, I have to test it with this value, and will update.
Many many thanks for your prompt reply.
I am also facing one more issue ( there were when i switched from iNav to Ardupilot many got resolved)