AltVario controls vertical the speed, not the power, so full power may be 3 meters per second up, and almost zero power is only 3 meters per second down (I forget the default). This is much slower than Manual thrust mode.
But (as a safety feature), if you move the throttle stick all the way down, the motors stop and it falls. So at 5% stick, it is coming down at a reasonable rate, and a tiny bit lower throttle and the motors stop.
And if your Input Throttle Neutral is set wrong, the motors may stop at a much higher throttle stick position. Typically, the Input->Throttle->Neutral should only be about 40 above Minimum.
(Edit: I didn't look at your config.)