I am having this issue in latest MP releases MP 1.3.56 and so on.
In previous MP versions, i plan Auto Missions with LOITER_TIME waypoint mode without any problem.
But now after updating to MP1.3.56 , i have confirmed a bug that my Waypoints Radius is set to a constant 45m irrespective of WPNAV_RADIUS parameter.
Solution # 01
I have to change Waypoint mode to WAYPOINT to solve this issue.
Solution # 02
I have to reverse back to MP 1.3.50 to use LOITER_TIME with normal waypoint radius.
Kindly look into this issue .