Same Issue Here.
I made a small SSTO with 2 rapiers and that worked fine, then made a bigger SSTO with 4 rapiers and a detachable ATV (Mun or Bust!).. FPS dies as soon as those 4 engines start. I thought it might be the higher part count, but the same plane with whiplash engines results in a much smaller frame drop. The difference is playable vs not playable. I Love LoVe LOVE this game. Hope the kinks get worked out soon.