Undeployed landing gear inside fairing = legs glitch all around

[Folkhoer]

I have this strange bug for a while now. By trail and error I know its the combination of retracted landing gear inside a fairing.
To make it easy:

Landing gear on my craft = no problem
Fairing (all sizes) = no problem
Deployed landing gear + fairing = no problem
Retracted landing gear + fairing = landing gear glitches all around and eventually explode.
This happens with all stock and modded landing gear.

So if I deploy the gear in the VAB (so it sticks out of the fairing) there is no problem, if I press G so it retracts it glitches all around.
Mods that I use that edit parts or have a big impact (I don't thing Kerbal Engineer is at fault here for example):
Beyond home
Restock
Everything from Near future