Would agree, but, check the building, see if it is actually operating at 200% efficiency. It's possible it's not, and is using the energy required to run at the speed it is actually running at, and not what is overclocked.
Such as, you have a mk1 that has max output of 90, you have it going into 3 assemblers, that all use 30 resources each per minute. That uses up the 90 that it puts out. However, then you add on the overclocking, and now it requires 60 per minute instead of 30, well, it's going to pull efficiency from the others, and slow itself down as well, and could, theoretically, without seeing the code and how they input it, bring down the cost of the energy demands as well, since the output can't pull enough to be 100% efficient across the board.
Just my opinion based on what I have seen, and since I have had to go and redo the whole network of manufacturing to get it back to 100%, too many times, and watched energy demands change as it went up, believe this to likely be the possible issue there.
Enjoy the game, it's popping on 5 of 6 cylinders as of the last patch!