A simple issue, the engine constantly builds up power when running on water and coal, only releases part of that power to the emerald kinesis pipe I have linked to a diamond one and a few resonant energy cells. This results in a permanent loss of a considerable amount of power, as the power stored in the engine starts draining as soon as I shut it off, but it doesn't output into the cells either. I have tried it with BuildCraft piping, Ender IO and a direct engine-to-cell connection, but the problem persists.

Normal operation of the Engines (BC engines historically always operated like this). As the internal buffer fills up, the Engine speeds up the pulses at which it emits power, eventually reaching an equilibrium where its outputting as much power as it is generating.