Thanks for the updates and suggestions people. I've done all the physics easing stuff and even tried using a mod that made the entire craft into one single unit instead of parts, yet nothing works. It seems when the wheels are involved, the clipping happens. I tried just parking the plane on the belly, and the "bounce after loading" issue doesn't happen. Also I've given an up tick to the bug tracker, and thank you for the very appropriate info SpannerMonkey.