The little room with what I assume to be the clown items named "???" poses to be a issue with the bots, and to piloting. It becomes it flooded permanently, and the bots fail to get to a hull breach affecting the room and freak out to the point of suffocating in a diving suit trying to fix it to no success. Other than this room causing some devious and slightly aggravating problems, this submarine has been a blast for my first time as captain!

It is intentional, at full throttle plus the anomaly you don't have enough power without the batteries, that's also why the light's green when it's off because it's only charging when it's off.

Ah, gotcha. Guess I'm taking my engie off reactor duty altogether then. ...and yep, that pretty much did it. Still have to keep an eye on battery power pull, but that seems intentional.

Only gameplay mechanic-affecting mod I've got in here is Retalented, which has a couple of it's own problems, admittedly.
Also I'm an idiot and assumed the battery switch light being green meant that it was on by default, didn't look closely enough at the labelling, so that helps a lot.
That said, the reactor really is way too delicate to have four slots - feels a bit misleading when it tries it's damnedest to blow up in your face the moment you plug a second rod in.

Nvm I was able to reproduce it and on more than just this sub, don't ever use the "operate reactor" command it apparently breaks every reactor a bot touches. The sub comes out of the box with auto control on so it shouldn't be necessary.

Do you have any mods installed, if not what are you doing when the reactor is overheating and what is the configuration of the switches on the bridge?

One sec lemmie take a look at this

Yeah, the AI insists on only sticking one rod in, and any attempt to change it results in them immediately changing it back when they're put back in charge. Might have something to do with the reactor seeming really prone to overheating. Even two rods requires CONSTANT adjustment for safe operation - which, again, the AI insists on switching back the moment it gets the chance. Don't play this solo unless you REALLY like baby-sitting a nuclear reactor.

The reactor doesn't seem bot-friendly; engineers have trouble keeping the power steady without some human intervention for some reason. Just a warning for the solo players.

camel MK jesus christ