Yeah, I was almost certain it is the new stuff, so whelp I guess
Edit:
Ok, so this is kinda stupid now. I have checked after some time, and there is stuff without a commander. Had to manually assign a CO about 9 times, half of those to Admin commands. I have hundreds of officers free. The Auto assignment WILL NOT ASSIGN to a post even if I can, most likely because the rank is higher than the one it is intended for (same reason why I asked/complained earlier). There are few officers with the right rank and no job, plus they have the right skill, but also other skill/s that are of a better rank so I assume the system does not want them wasted (like 20% log and 25% mining so they were NOT assigned to a freighter) and thus does not post them there. Kinda bummer.
If it makes me mad enough I might try booting vanilla Aurora and checking if it is truly a bug (probably not a bug but rather oversight/design decision), since I use AuroraMod. Though it might need some creativity that might be hard to do in order to simulate those situations.
Edit2:
Actually, I have a free position of Commodore for Geosurvey section. Even a free Commodore with 30% Survey and everything else at 25% or less. The Auto assignment still hadn't posted him there for some reason. The only thing stopping that might be 50 training he has, but I do not value 50 training higher than 30% survey AT ALL, I hope the game doesn't either (or it does because it uses simple number comparison to get result and Training is the one that is different to the rest of skills).