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Also noticed this problem popping up again the other night. Haven't had a chance to do thorough testing and this is all from memory but I had a small probe in a low, slightly eccentric and inclined orbit (<30km) around minmus. I noticed while at/near the periapsis and apoapsis, the opposite side would vary in altitude while in normal time mode. Over the course of 30 seconds it swung wilder and wilder up and down to the point where it was gaining or losing hundreds of meters every few seconds. On rails time warp would stop it and seem to temporarily dampen the wobble after returning to normal time. My craft in this case had no wheels as the others have suggested might be the cause. It was a okto1 probe core with two oscar-b fuel tanks and an lv-1 ant engine. tri-symmetry lt-05 micro landing struts, tri symmetry 1x1 solar panels, some small science attached to the probe core and a z-200 battery attached to the top node. Only odd thing is a tt-38k radial decoupler than remained on the side of the probe after detaching from a larger probe launcher. I only say odd because it makes the probe slightly off balance and causes minor issue with holding a course during a long burn.