I haven't found a solution to this problem, but I as well have encountered it. When attempting to time warp, whatever ship I am controlling instantly explodes, with structural failure from what looks like every joint. I only have Kerbal Alarm clock installed, and I can't remember if I encountered this glitch before I installed the mod or not. It seems to be fairly intermittent, and I usually just quit/restart and it stops happening, however recently it is more consistent. I have a ship that recently undocked from an orbital station and I have two planned maneuver nodes. I can time warp to the first node, perform the planned burn, then when I try to warp to the second the ship explodes. When I quickload the game, the ship explodes at the first attempt to time warp to the first node. I haven't tried to delete any physics files or anything of that nature. I just recently found out about the alt-f12 menu from reading these threads as well. I'd happily supply any further information, just may need to be specific on what info/screenshots you'd like, and sometimes how to show that information as well.