I tried looking at the problem a bit closer, and although it isn't fixed, I think I might know what it is.
I was working on a Lander using the “Hecate” and the “Erebus”. The Hecate is the smallest vacuum optimized engine that uses liquid hydrogen, the Erebus is a larger sustainer. I opened up this waterfall window that you get by clicking on the box. The Hecate has two effects in the waterfall window, but for some reason the Erebus has no effects. I tried reinstalling the mod a few times and it didn't fix the plume issue. However, when I first installed it there weren't any engines, but reinstalling it added the engines.