same here, this is one of the aspects of the game that seems permanently bugged.
you can switch which systems you want active during emcon here, but you’ll have to click each system several times, because the grey emcon icon resets every time as soon as you leave the power room; whenever you return to the power room, all systems will show as emcon disabled if you’re currently not in emcon, and all systems will show as emcon enabled if you’re currently in emcon.
additionally, while the game does remember your settings even when the icons immediately break again, this also gets reset any time you leave the game. so anytime you restart the game (including after one of the frequent crashes) you have to click each system several times again to set it up properly.
there are also two other related issues on this panel:
it only supports viewing a maximum of 12 systems in total, but all ships can have more than 12 systems installed. so you won’t be able to set emcon mode or check status here for all your systems from 13th onwards, you will instead have to manually disconnect or reconnect them from the engineering screen, depending on their default setting. this is only dependent on the order you install them in though, so if you sell one of the 12 shown system, the 13th you installed with be shown then, and so on.
exacerbating the issue above, is that the default settings for some of the systems don’t make sense, imo.
countermeasures are emcon disabled by default, even though they have very low emissions, and can be critically important to avoid an incoming torpedo – which, incidentally, is also one of the situations for which emcon mode is used.
jump drives are also disabled by default, despite the fact that they have zero passive emissions or power drain. they only have very high values of both for a short duration right after you activated them manually from the helm, and can be just as easily deactivated again right from the helm, no need to switch to the power room panel for that. and if you did just activate them – like to make an emergency jump when there’s pirates incoming or you want to avoid a patrol that might detect your contraband – then you’ll probably not want to have them turned off while you’re trying to evade other ships until you’re in a position to make the jump.
sensors on the other hand are by default emcon enabled. which is fine if you have one of those amazing low-emissions sensors, but a bad idea with most others. the starting sensors of your ceres actually have the highest passive emissions of all your systems.
sooo… in short, there’s a lot that needs fixing/improving regarding the power panel and setting the emcon mode of individual systems. on the bright side, i think none of these individual issues should be all that difficult or time consuming to work out. just a question of whether they are a priority over the many other issues this game currently has.