In 64-bit KSP 1.1, with only one mod (the docking alignment indicator) - launching a fairly large rocket (174 tons in 6 stages):
If I save and then attempt to load the vehicle, it shows up on the vehicle list as "116 parts in 13 stages", but there are only six stages on the sidebar.
I click "launch". I go to the pad. If I don't do anything for a few seconds, the spacecraft settles in. It appears to be intact, but the first three stages disappear from the stage sequence on the left. If I activate the staging sequence, I get the fourth stage.
If I hit the "stage" button before the rocket "settles in", stage one fires as it should, but controls then appear to be locked.
I have checked visually - in both of these scenarios, the rocket appears to be intact, just the controls are misbehaving.
If I leave the pad after the rocket settles in, then come back, the top half of the rocket falls to the pad immediately upon my return and lights everything on fire. I do not see the bottom half.
The spacecraft in question has three probe bodies and no crew.
I have tried quitting and reloading, shuffling the stage sequence, and similar with no apparent effect.
Has anyone seen similar behavior? Any idea how it might be fixed?