Your mods are awesome by the way. I have a ton of mods installed so that's very possible but I wasn't able to find a patch related to the engine.
None the less I did fix it. Turns out the Scylla was not exhibiting this behavior because it generates EC (not sure if that's a mod or not). I do have System heat and NFE installed. I was able to fix it by making the Deliverance generate EC. The root of the problem was the reactor power would sit at a low level when enabled and no fuel flowing and would need to ramp up when fuel started to flow. When it generates EC it ramps all the way up to full reactor power without fuel flow.
So it seems like the collision of a bunch of mods. My fix isn't the right way but it works and if anyone else runs into this it might work for them too.
If you're bored I can send you my mod list, but since it's fixed no need to waste anymore of your time.