Hopper pairs STILL duplicating items as of 1.11.2

I see lots and lots of pre-existing item duping bugs listed on MOJIRA, all of which are "fixed" as of a 2013 snapshot. I'm a co-operator on a vanilla 1.11.2 server hosted at mcprohosting.com, and we're seeing this problem on a daily basis in 1.11.2.

I've built a mob farm that uses three hopper clocks. Two of them don't bother with the pistons and redstone blocks because what I want is a single item going back and forth between two hoppers pointed at each other. In much less than a day, the machine can stop working because both of those hopper pairs end up with duplicated items in them. Thus I regularly have to go in and clean them out.

I realize that 1.12 is your priority. But since 2013, this problem has apparently been off your radar as "fixed," so its very unlikely that this has been looked at at all during the 1.12 development period and is therefore not actually fixed in the latest versions.

I would like to be able to tell you more about what's going on, but I'm going to have to wait for your questions. Shortly, I'll be able to get at the web console for configuring the server, in case you want to know about any special settings there might be. And if you coordinate with me, I can arrange to set someone from Mojang into spectator mode or whatever they need. I can post the address in a comment, as long as that's not against your rules.

On this server, one of the clocks is located at -459/114/220, and the other is at -459/114/216. There is third one in between, which does not seem to be duplicating items. And note that these are not straddling chunk boundaries or anything. They are located in a busy area that may be getting loaded and unloaded an awful lot.

I think that they may be just outside of the spawn chunks, but I'm not 100% sure. I assume that if they were inside of the spawn chunks, they would never get unloaded, but I'm only guessing that loading/unloading has anything at all to do with this. I haven't noticed this happening when I was AFK near this, only when I've been logged off for many hours.

One other thing: This world was originally created on someone's PC and shared to the Internet. Shortly thereafter, it was imported into mcpro. I would not expect this to matter, but who knows.