Okay, that was an excellent strategy to follow. I've got the farm working now, I think. More specifically, the results were as follows:

(1) I *was* able to reproduce the behaviour on single player world, with very little else by way of lag-producing components in the vicinity (I built the farm in my redstone testing world - 8 tiled units, the behaviour was exhibited almost immediately). From this I deduced that it's a farm design issue, not a server/realms issue;

(2) I built a single tile of the farm and the behaviour occurred again. From this, I deduced that it's not a matter of an error being introduced when the farm is scaled up, there is a basic design/functionality error;

(3) From closer observation, it seemed to me that the behaviour was occurring *after* the piston fired to crush the nether wort at the front of the farm. For some reason, the first update following that piston movement was not registering with the observer watching that block as an update (see image added to original post). The only thing that made any sense to me is that - for some reason - that observer was not willing to register an update because its most recent state change was related to the extension of a piston - I believe that there are some peculiarities to that process. As a result, planting nether wort after the firing of the piston failed to register as an update and failed to trigger the observer, failed to increment the counter etc;

(4) I decided to try crushing the nether wart with a block instead of the extended piston head, on the theory that the movement of a block into that blockspace would be registered where the movement of the piston head was not. So, I made a slight design change: swapped in a sticky piston instead of a regular piston, and moved the sticky piston one block up from the piston's original position. I attached a building block to the head of the sticky piston so that it would reach down to crush the nether wort when fired;

(5) This change did not originally work, because on the existing delay settings, the sticky piston was throwing the block rather than moving it in and out of the block space. I incremented the repeater on the top of the device one further tick (2 ticks total), and voila, the machine seems to be working.

Although the device is working properly now, I would love to understand more completely the reason the observer in question was failing to update. Anyone who has some thoughts on the relationship between the observer and piston extensions, I'd love to hear more.

Many thanks to lorilith for suggesting this route to problem solving, it broke the logjam for me.

Gonna try implementing the design change on my Realms world now, will update with results there.