Kerbal Space Program

I encountered this problem when trying to do an Apollo-style Duna mission. The burn time indicator thinks that the engines on the lander craft are enabled (even though they never were, I think that the game thinks I staged them in a different order because they first time I staged after redocking it didn't do anything, and the second staging decoupled the booster, but if the burn time indicator counted the staging differently maybe) and since the lander craft engines face opposite to my main nuclear engine, the burn time is projected for the net thrust from burning both engines at the same time. Enabling and disabling the engines fixes this, but after docking and redocking the two craft, the burn time indicator goes back to thinking that the engines are enabled.
Included is a video, there are mods displayed in the video, but I've been able to demonstrate the issue occurring on a non-modded install on a different computer, so keep that in mind when watching the video.
A quick workaround is to drag the actually enabled engine to the bottom of the staging list, but this has to be repeated every time the vessels are docked.

Video of the bug in action: https://www.youtube.com/watch?v=6IxAB85eXM0