Maybe SetPrimaryPartCFrame interacts weirdly with seats. I wouldn’t recommend it anyways, since it has some issues with precision over time.
Does it occur if you just set the primary part’s CFrame directly and let the WeldConstraints solve the rest of it for you (and are they WeldConstraints or Welds, because that might matter too)?
Could you maybe record a short video of the problem occurring? It’s somewhat hard to tell.