Hitbox on the landing gear was probably changed slightly and no one noticed. All of the symptoms mentioned point towards geometry issues with the ship.
When you recall your ship the algorithm that decides where it lands gets to determine every possible position from every possible angle before picking a spot, in a fraction of a second, so naturally it'd seem like it was working fine when that feature is used. A computer is triangulating by the hard mathematics of the terrain, not squinting through the cockpit window and trying to make an educated guess about the radar.
On the bright side you've got plenty of hull, so you can always try the noob trick of grindin' 'til she sticks without any serious consequences.
When you recall your ship the algorithm that decides where it lands gets to determine every possible position from every possible angle before picking a spot, in a fraction of a second, so naturally it'd seem like it was working fine when that feature is used. A computer is triangulating by the hard mathematics of the terrain, not squinting through the cockpit window and trying to make an educated guess about the radar.
On the bright side you've got plenty of hull, so you can always try the noob trick of grindin' 'til she sticks without any serious consequences.