Summarizing a discussion on IRC: this is a symptom of forces being applied using RigidBody.AddForceAtPosition, instead of Part.AddForceAtPosition. The latter (added in 1.2.x) allows other mods (such as Principia) to inspect the forces that were added; Principia needs that in order to be able to integrate the overall motion of the vessel; any forces added via the former will have no net effect on the vessel. Note that rocket engines, AJE jet engines, FAR aerodynamic forces, etc. use Part.Add
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