As a short term solution i resolved this issue by editing the config file for the LT-2 Landing Struts, the ones that gave me the most bounce on load issues. I changed damperRatio = 1 to damperRatio = 10 and this caused the strut to spring back quicker which solved the problem. Maybe the force of the bounce is relating to the length of time the part is clipped? Might be why the problem is more pronounced on heavier ships.
G:\Steam\steamapps\Common\Kerbal Space Program\GameData\Squad\Parts\Utility\landingLegLT-2
Relevant lines:
targetPosition = 1.0 <-- not sure
springRatio = 6 <-- when set to 0 the strut sags to the ground, I think a high number would make them ridgid(maybe they would break on landing)
damperRatio = 10 <-- at 0 the bounce never ends, at 10 it stabilizes quickly with minimal bounce
boostRatio = 0.6 <-- not sure
