Hopper Clock Item Duplication in Realms

I built a wither skeleton farm on our realm. It incorporates a simple hopper clock (2 hoppers pointed into each other with 9 stack-able items placed into them, feeding into comparators powering sticky pistons moving a redstone block) to control the movement of captured ghasts that serve to sweep monsters off the spawning pads.

After a while the ghasts started making their passes at longer and longer intervals. Upon investigation, I found that there were almost 3 stacks of slabs in the timer, rather than the 9 I placed there. I assumed it was a mistake, cleared out the extras, and thought no more about it... until I had to clear it out again a week later. I tested earlier by swapping out the slabs for 9 of my growing collection of wither skeleton skulls, and within less than an hour- with me the only one online, there were 10 skulls.

In retrospect, I suspect that this bug is what caused my old iron farm to fail several times, as it used the same type of clock to regularly fire flowers into a nether portal to keep the spawn chunks loaded. If this bug was active at that time the clock must have gradually slowed until it allowed the chunks to unload, at which point the multi-village stack of cards collapsed.

Steps to Reproduce:
1. Build the simple hopper clock described in a Realm.
2. Kill time, maybe runaround a bit to let it load and unload.
3. Profit?
4. Honestly, I'd rather the clock worked properly than use it to duplicate items, particularly since I have to keep adjusting a machine that should be self sustaining and since I think it wrecked a previous project of mine.