That was along the lines of what i thought of initially, but apparently the engines itself don't burn-up any EnU during operation and run just fine even without it. Did you include EnU for engines that don't have a functional (or rather usuable) reactor for...i'm lacking a better word here...aesthetic purposes? Also, shouldn't taking 1% of full reactor output reduce thrust by approx. 1%, instead of increasing the burn-uprate of the reactor fuel? Like i stated before, if you compare the stand-alone reactors and the engines, the effective run-times seem to be way off - the reactors can run years at 100% output, while the reactor modules of the engines struggle to run more than a few months at 1% output. At least that's the case for the smallest reactor+engine, but the burn up rates for fuel in the engine(-reactors) are in general about 3 magnitudes higher than they are for the stand-alone reactors.
I've superficial knowledge of reactor and engine design at best and i can't tell if this is simply due to limitations of what's possible in KSP (i.e. making thrust fuel level dependent), but it simply strikes me at odd. Don't get me wrong, i'm not trying to talk down your mod - the whole NFE series is an excellent piece of work; i'm just trying to figure out why you implemented it this way and how i can best use the engines and reactors in the game.
BTW, what is the second option in the advanced reactor control panel for? The first one controls shut-down temperature, but i can't figure out what the other does.