I had the same symptoms after I upgraded SCANsat from 8.1 to 9rc4.1, but at the time I just assumed that it was because of incompatible versions. After restarting the game some of my ships just lost most of their joint connections and multiple RCS exhausts are coming from odd places. I saw this thread and tried updating Tweakscale, but that didn't work. Currently I have removed SCANsat 9rc4.1 fully and for now everything seems to work. Here is my current mod list: Aviation Lights 3.7 Crowd Sourced Science 1.4.0 Docking Port Alignment 4.0 In Flight Waypoints 1.1.1 Infernal Robotics 0.19.3 Karbonite 0.5.1 Kerbal Alarm Clock 3.1.2.0 Kerbal Attachment System 0.4.10 Kerbal Engineer 1.0.14.1 Module Manager 2.5.6 NEAR 1.3.1 Near Future Construction 0.4.0 Near Future Propulsion 0.4.0 Near Future Solar 0.4.0 Precise Node 1.1.2 Procedural Fairings 3.11 Toolbar 1.7.8 Tweak Scale 1.50