Mode changes to ALT_HOLD from LOITER with gps arming check disabled

I am using 3DR Solo (copter 3.3) for indoor autonomous flight using motion capture data. My step 1 in this direction is to takeoff the uav in an autonomous mode - loiter/guided without gps.

For that I disabled the gps requirement - ARMING_CHECK = 0, FENCE_ENABLE = 0. Even after these changes when i arm the uav the copter-3.3 firmware displays “EKF_Variance” warning and changes the mode to altitude_hold (mode in which I cannot do autonomous functions). Also if i takeoff the uav in alt_hold mode then try to switch to guided mode i am unable to do that. I believe this is due to ekf_variance check

Any idea on how to disable ekf variance check ?