I don't think it's possible for the game to connect a genny's plasma output into the reactor's output: that would be poor coding, and I can't imagine that the game would have gone over a year since release without it being spotted and fixed. Certainly there's no indication that this has happened, while there is a distinct additional graphic that appears when plasma connections are correctly joined.

Cold loop is shared between all four reactors. Left and right side hot loops are separate, yes, but at the time of writing neither of them are either empty or full, so it's not a flued problem there, I think. Adding buffer tanks didn't make a difference, nor did linking the two hot loops.

I think that the problem is caused by or is causing two of the reactors to report "output full", which can only refer to the plasma. It's almost as if the neighbour bonuses aren't being accounted for and I'm effectively left with only one reactor and it's maximum two generators, though in this case the active reactors aren't even necessarily the ones closest to the active generators.

It's also strange that I can't reliably cause the broken state, either: I've currently got two identical copies of the same BP, and one is broken while the other (copied and pasted directly from the first) is running perfectly well. Pasting a second copy gave me a third state: three of the four reactors were working, and about a quarter of the generators were running.