I have never seen such a large issue as this but here is a possible reason.

The modeler animates the landing gear for a certain distance of total movement in the suspension.  If the contact points are set correctly, this exact movement is used by the sum of static compression and the distance represented by max to static ratio.

When the aircraft extends gear for landing, the suspension is fully decompressed.  As it settles onto the runway, some compression takes place, but lift from the speed and flaps will not allow it to settle to normal static compression until speed is reduced or flaps are retracted.

If the gear eventually settles to the ground, then it would seem possible that the total compression animated does not agree with the compression stated in the contact points.

It is also quite interesting to check to see where FS thinks the bottom of the tires are.  You can find out by using a nav light in the Lights section.  Set its coordinates to the same numbers you see in contact point 1 or 2 if that is the main gear points.  Watch that light during a landing operation to see what happens.  It should be a telltale sign.

Have fun.