I'm having a somewhat similar issue. My cockpit in on a string of pistons with the thrusters at the other end. If I turn the dampeners on, which I kinda need for flying in gravity, the pistons start moving like an accordion as all the thrusters alternate firing. I've tried different combinations of "share inertia tensor" on varying/all pistons but that didn't help. Would love some suggestions as to how to fix this, please!

Also, Whip, you and your collection of mods are amazing!