Just a quick question. Is the ground base (that you are attaching the pylons "buried" in the ground (ie. you didn't use the "surface attach" when placing it on the ground)? If that's the case then it will cause some crazy physics issues, also, are you using a ground base or something else that can be attached to the ground? If you are using a ground base I recommend that you unattach it from the ground, reattach it, then try again. I know that when a new patch comes out that some of the KAS stuff from an old save file might freak out if the parts used were tweaked.
Sorry to hear about your Space Kraken problem :(