It appears that in MI 1.6.11, neutron flux / generation is now somehow linked to restarting the game.
Attempting to start a reactor with any amount of fuel rods will only have neutron flux remain around -0 to 0.1, and it increases only after restarting the world.

Also notably, if the world is restarted enough times that neutron flux is at a high level, the rods can be removed and the neutron flux will not drop. The reactor won't produce steam in this state, but deuterium/tritium will still be produced.

Initial

1 restart

2nd restart

7th restart (approximately normal equilibrium)

The rods can be removed and the neutrons remain.

Although the nuclear reactor is still, in a way, functional in single player, needing to restart a multiplayer server repeatedly isn't great...

Reproduced in a 1.19.2 instance with MI, Fabric API and Cloth Config.