Gastoff, The problem with your aircraft is it's re-loading itself in 'Static height' position and then jumping to 'Wheel Height' position. The only fix I know of is to adjust the static height to match the wheel height. This may take some tweeking in your aircraft.cfg file.
Start the sim with another aircraft, hit pause 'P', change to the problem aircraft via the toolbar. Remain on pause and view the plane. If it is hovering above the tarmack adjust the static height slightly down, if the wheels are sinking in the concrete adjust static height up. When you release pause the plane should bounce into the correct position, that is 'Wheel Height' (assuming the wheel height is set correctly).
[contact_points]
//0 Class <0=none,1=wheel, 2=scrape, 3=float>
//1 Longitudinal Position (feet)
//2 Lateral Position (feet)
//3 Vertical Position (feet)
//4 Impact Damage Threshold (Feet Per Minute)
//5 Brake Map (0=None, 1=Left, 2=Right)
//6 Wheel Radius (feet)
//7 Steer Angle (degrees)
//8 Static Compression (feet) (0 if rigid)
//9 Max/Static Compression Ratio
//10 Damping Ratio (0=Undamped, 1=Critically Damped)
//11 Extension Time (seconds)
//12 Retraction Time (seconds)
//13 Sound Type
//14 Airspeed limit for retraction (KIAS)
//15 Airspeed that gear gets damage at (KIAS)
point.0 = 1, -25.0, 0.0, -17.5, 1000.0, 0, 2.0, 70.0, 0.5, 3.5, 0.900, 9.0, 8.0, 0, 220, 250
point.1 = 1, -114.0, -18.0, -21.3, 2000.0, 1, 2.0, 13.0, 3.0, 2.5, 0.900, 11.0, 9.0, 2, 220, 250
point.2 = 1, -114.0, 18.0, -21.3, 2000.0, 2, 2.0, 13.0, 3.0, 2.5, 0.900, 11.0, 9.0, 3, 220, 250
point.3 = 2, -152.6, -103.5, 3.0, 700.0, 0, 0.0, 0.0, 0.0, 0.0, 0.000, 0.0, 0.0, 5, 0, 0
point.4 = 2, -152.6, 103.5, 3.0, 700.0, 0, 0.0, 0.0, 0.0, 0.0, 0.000, 0.0, 0.0, 6, 0, 0
point.5 = 2, 3.0, 0.0, 0.0, 700.0, 0, 0.0, 0.0, 0.0, 0.0, 0.000, 0.0, 0.0, 9, 0, 0
point.6 = 2, -222.7, 0.0, 4.0, 700.0, 0, 0.0, 0.0, 0.0, 0.0, 0.000, 0.0, 0.0, 4, 0, 0
static_pitch = -0.5
static_cg_height = 17.5
gear_system_type=1 //Hydraulic
On this FS9 default 747-400 the nose wheel is at -17.5 and the main wheels at -21.3
Like I say, it takes some tweeking to get it right.
I hope this helps or maybe someone else has something helpful to add. Good Luck.
P.S. Maybe you should remain in cockpit view while your passengers board to prevent any injuries.