Tried the update out to see if the primal enchant and efficiency enchant worked together and they still don't.

I also tried to make a new revolver to see if the fix wasn't retroactive but with primal and 2x efficiency it was still using 2 essentia per shot.

What are levels of both primal and efficiency on the revolver?

My old pre fix revolver I had was 1x primal and 5x efficiency, and it was using 2 essentia per shot. I made a new one, in case the fix wasn't retroactive with 1x primal and 2x efficiency and it also was using 2 essentia per shot.

I'm using ThaumicBases-2.1.189.32, and I have a revolver with both Primal I and Efficiency V.

I can get two shots from one essentia, but after every two shots, the gun goes "click" when used and just rotates the cylinders.

Yes, that is what is supposed to be happening - the reload each 2 shots. I still can't track the bug down, or even prove it's existance...