That happened to me too. To the creator of MechJeb, can you please reprogram the deceleration of the time warp so it clicks down at a slower speed? Because currently, the whiplash of the sudden jump from hyperspeed to 1x speed is causing rockets to rip up. Also I've found a bug where SAS won't turn off while transferring between planets during warp to course correction burn, and consequently the warp no longer works, meaning that you have to abort the trip and go around the sun for at least another lap before doing it again.