I'm usually not one to post craft files, but I have no idea what is going wrong with this craft. When in space at 1x time acceleration (using Better Time Warp), the craft has a phantom force applied to it accelerating it directly upwards (against the force of gravity) at approximately 5m/s^2 (at Kerbin). It may actually be exactly half of the force of gravity, though I would have to do additional testing to confirm this. The effect also completely disappears at 2x time acceleration or higher.
I'm a veteran player and I've seen kraken drives before, but there shouldn't be anything on this probe that could create a kraken drive.