I figured it out. The same thing happened to me when I was flying my SSTO and all of the engines were in the same stage and I would just activate and inactive them whenever. You have to separate the engines to a different stage.
For example, I had all of my RAPIER engines in one stage and the Necular engine in the same and it was showing the burning time if I used both of the engines. All you have to do is to move the engines to different stages so when I did was move the nuclear engines to the first stage and the RAPIER engines to the last.