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To get KJR working, you can change <bool name="multiPartAttachNodeReinforcement">1</bool> from 1 to 0 in KerbalJointReinforcement/Plugin/PluginData/KerbalJointReinforcement/config.xml Explanation of all the options in the readme.

When I loaded a game with Cryo Engines and Tanks, it removed all active contracts, my contract history, prevented new exploration contracts from appearing, and duplicated the Advanced and CommNet difficulty options. Thankfully it wasn't an important save, just a temporary one while 1.2 mods are updated. Removing the mods and reloading fixed it.

I may have found a temporary fix! Hangar Extender (1.2 build here) seems to sometimes fix it. It doesn't work all the time, but if you go back and forth between VAB and no-VAB, or go to KSC and back to the VAB, it'll fix it until you launch or exit. It also brings up this message in console: BoxColliders does not support negative scale or size. The effective box size has been forced positive and is likely to give unexpected collision geometry. If you absolutely need to use negative scaling you can use the convex MeshCollider. Scene hierarchy path "launchClamp1/model/launchclamp/obj_girdercap/obj_girder/obj_girder_mesh"