I put a feeding station on each floor I want the Pals to do things, that seems to keep them finding things. The interesting bug is that since two ranches are on the second floor, while I'm logged out, the stuff in the ranch has a tendency to fall through to the first floor.
I have a similar base minus the walls, I also experience this when I warp over sometimes.
One time I warped in and I observed my whole base loading in. As it happened, my breeding-floor pals fell and disappeared into the earth once the foundation loaded. Quick resummon, but I frick'n cackled at 2am