Why do Engines fire on inactive craft in the background/when I load a save?

[DerGolgo]

Right, couldn't find this. Not yet requesting "support", trying to figure out what I did wrong, first.

Here's what's been happening: I build a massive ship to go to Duna. Sandbox mode. Assembled it in orbit. Finally bring the crew. Docking doesn't go as desired, so I load the save I made on approach.
When I saved the game, the engine on my little crew transporter was shutdown.
But when the save loads, bam, it also fires the engine - and won't accept any input to shut it down until it's done with all the loading thingies. While the craft is already accelerating.

And that is not all. Eventually, I build a simpler, huge craft. Just want to get going, no 2nd round of assembly, plop into orbit with hyperedit. When I leave it there, it's just sitting there. Pointed to normal, engines never activated in the first place.
Then I launch my lander craft, which I DO want to dock in, I wiggle through the transfer orbits and, finally, on closest approach ... my massive ship just zips by, engines blazing.
I go to tracking station, switch vessels and shut down engines. Lucky me, the engines were blazing on no throttle. But still, this is too similar to be related.

Some setting I messed up? Some way I never found to lock an engine so this won't happen?

EDIT: Just tried it with switching vessels from the orbital view. Here, too, my big ship's engines (Emancipator nuclear engines) ignite while the little green messages are zipping up at the top of the screen. Switching back to the lander craft currently in a lower orbit, I was already hammering my "kill switch" (key assigned to shutdown all my engines through AGX action groups), so the engines didn't fire there.
Tried switching vessels back and forth once again, without touching the kill switch. This time, no undesired ignitions to be observed. I think it may be something when the craft is first loaded during a flight?

Edited January 27, 2017 by DerGolgo
Further observations

[Benoit Hage]

We need to know at least what mod you are using.

[DoctorDavinci]

Go to your settings at game startup and move the slider for default thrust on load to 0 (I think that is what it is called ... look and you'll see what I'm talking about)

Hope this helps