Another possibility is that since you changed to position of the wheels, one of the previously defined collision boxes (fuselage or landing gear) now intersects with or is below the tarmac so a collision condition is reported and needs adjustment.
There are no collision boxes in Aerofly FS. All collisions are computed based on the actual 3D mesh of the airplane + manually TMD defined wheels.
The flips or glitches come from an ill-defined joint. Check the joint multis and reduce their Kd and Kp values. You can make then rigid for now to get away from the issue temporarily, with input lock 1.0: