I created the following reactor:
The first run it produced 60 EU/s, which it should 3*4*5=60. However, after cooling and reloading the reactor it only produces 30 EU/s, I have two reactors running this setup and they are both producing only 30 EU. I have tried removing the cells and replacing them, as well as exiting and restarting the game to no effect. I did not use any mods such as TMI to get the cells, all of the cells were acquired via enriching isotope cells in a breeder. That is the only difference between the first and second runs; I merely let them cool and replaced the uranium, this time using cells acquired from a breeder instead of ones crafted with a uranium ingot.