This problem happens in both Linux and Windows. I use Windows at work and Linux at home. I use Dropbox to sync my game files. The only mod I use is MechJeb for the tedious bits. Career Mode.
Situation: I built a large base to meet the career requirements for the mission. The last piece I added was a fuel buggy to refuel ships. I used the grapple because all other attempts to match the buggy using the Docking Port Sr. failed to connect. I joined the fuel buggy to the base by having the grapple grab the docking port Sr. During ground testing the worked fine. Memory says that I even tested it at the Mun, but I can't be sure. After the sky crane (like it sounds, a drop ship) detached and left, when ever I tell the grapple to release, the buggy goes sky high and destroys itself. I have tried everything I can think of to simplify the system by removing extraneous items, stopping drills, even detaching section of the station, completing other missions, and reloading at different points. Nothing helps. As soon as I release the grapple, the fuel buggy flies apart.
Is there a way for me to send you the save file so you can check the physics or attachment data?