Captain doesn't accept orders after boarding, or vanishes when changing

[XenonSurf]

Playing XR 3.53 with mods (see list at the end).
I guess this one must have been already reported, but I didn't find it after a careful search.

I have used the mines of a Traitor Drone on a Rahanas that was isolated in a zone, but still in the zone. I then boarded the ship which was successful.

Now, maybe this was wrong, but I first have sent the Engineer inside the CAP, then the Captain and the Defense Officer, skipping the Guidance telling me to first send the captain.

Problem 1:
I realize that the captain tries to accomplish the last order that the ship had before the boarding (trading with a station in another sector) and it's NOT possible to give him any fleet orders, fly to, join my squad, leave my squad.
I then changed the captain with another and better one that I had on my Skunk (I play with MoreCrew mod) and the situation was resolved, the new captain accepting all orders.
The odd thing is: if I again change to the other captain (for selling my ship because I want to keep the better captain that I have trained), then I have the problem again and I CANNOT sell the ship if I go to the dealer.
Eventually, I fired the 'mutiner' captain and sold the ship with the better captain onboard

[Probably solved]
Problem 2: Ghost Captain
After a boarding, from the CAP, I have remotely called another captain that I had onboard the Skunk, I had to leave the bridge and return on the CAP to speak with the new captain. Now, I realize my other captain has VANISHED He has not returned on the Skunk. I remember this has also happened when I sent a better pilot to a small ship, the other one just has vanished in Nirvana...
If I change the captains from the Skunk instead, the captains change place normally without one vanishing.

My mods:
Litauen_Capital_Ship_Bridge
Mission_Computer_v133
Mission_Computer_Removal_v113
More_Crew_v135
Nidaren_Titurel_Engine_Fix_v106
w.e_BetterAutoAim

Is this due to a mod or is it a bug that will be eradicated in future patches?

Thanks,
XenonS

[XenonSurf]

Problem 1 has gone when I load one of the last Autosaves, so I guess that if I restart the game the problem magically dissapears.

Problem 2 is solved, as the captain which I sent away was in fact in the crew quarter of the ship bridge mod but somewhat hidden and hard to find in the first place

XenonS

[strude]

I always assumed that the captain listed after a boarding is more or less a temporary place holder until you supply a functional captain. Maybe the marine officer assumes command to keep the ship steady or something.

I don't think I've ever got the "after boarding" captain back when assigning a captain to a captured cap.

[XenonSurf]

I have done a couple of boardings since then, and the problem 1 didn't show up again. I have a Titurel and 2 Rahanas, I changed my captains to have the best of them placed in the Tit, also did other crew changes, but I have done all this from the Skunk and from the menu: you cannot recall a captain from a CAP, but you can change him if you want, so I hired another captain, then I moved in the Skunk's crew quarters to send/change him and other crew in the CAPs.
No problems anymore since then.

XenonS