Ditto. I thought it was related to my earlier portal problems, but perhaps not.
For me, they disappeared from the screen and minimap (I think, I'm uncertain about the minimap but I believe so) and as far as I could tell simply weren't there at all rather than not visible. They were still visible on the world map though. I didn't investigate too thoroughly since I thought it was just me. A quit and restart fixed it.
Could they be being mistakenly removed by the entity cleanup routine you put in?
//TODO: Insert witty one-liner here.