what if you did a setup like this:
Where chests are actually fence posts?
It used to be a solution to a similar problem with mobs phasing through fence posts when chunks were unloaded/reloaded.
I just remembered having this same issue whenever the server resets while I'm grinding in the skelly/spider farm. If there's a surplus of skeletons waiting to be killed, when the server comes back up a handful of them have escaped into the room with me.