May it be, you have the mod multiverse installed?
had the same problem but after deleting the mod data, everything worked fine again
Okay after some testing it seems that the sector with captain controlled playerships gets unloaded if the player jumps 3
multisectoring worked after i jumped out of the sector
multisectoring worked after the next jump
after that jump i did not get any materials.
Some more testing later
i had to creat a new galaxy, with no mods installed and multisctoring works fine