I have a similar issue.
Destroyed those protective walls in my room and left the room with a creep.
Leaving the room worked well, but going back to my room, doesn't work.
Left the room, if it was FIND_EXIT_BOTTOM in the code below, but in next room this it moves to the exit, but does not move to the next room.
creep.move(TOP); while standing at the exit returns 0, but doesn't do anything.
var exit = FIND_EXIT_TOP;
creep.moveTo(creep.pos.findClosest(exit));
My room is E5S2 and trying to enter from E5S3.