Something I noticed a while back (at least a few updates back) was when I had an automatic wheat farm it worked great all the seeds and wheat made it to the drop off point. Then a few updates back a while after the grouping started only on EMC, I believe it was made by Justin/Aikar so it was only on EMC (Before mojang decided to make something similar just a crappier version of it). Around then I believe after the mojang version was implemented (as in a month or so later?) the water currents wouldn't pull all the wheat/seeds to the end area. They were literally stuck going back and forth in a small area in the water current and the only way you could get them to move was to get closer to them. So you had to be within 5-10 blocks for them to move properly. I think that was something to do with Aikar changing the code a bit or something so that way you had to be within so many blocks for items to update or something. I have since destroyed my wheat farm because it was in the way of other stuff and haven't made a new one but I believe it applies to what is happening here. And I believe a while back the grouping became worse on EMC it wasn't grouping them as well as it had before so that also could be a factor.
Meh, this is all mumble jumble to. Just try looking at different versions of how to make the farm to be automatic. Now, it could also be that the seeds and wheat are getting "stuck" on the lip of till soil, if you just have the farm floating in mid air. This causes some items to fall, out of range of the other items grouping together. It's happened to me before, but not when I built it underground. Though, when you build it underground, it still needs a decent light level. The time you didn't collect the wheat doesn't matter as long as it was fully grown at the time, and there is a variable of how much wheat AND seeds you could get from one, so each total yield will be different, and not exact. This also causes problems when trying to create ratio of how many wheat for how many seeds, as there would be a lot of different true ratios, with...
You are harvesting faster than the code can produce a response. When you hand pick the produce, it allows the code time to reset. Every request sent to the code is sent in packets over the network. Some of them are getting lost on the way due to connection speeds. You found the limit by expanding your farm to full res.
Your problem might have something to do with how long it takes for everything to flow down to the collection area.
This is the Entity Activation Range causing that problem. It's SUPPOSE to not affect stuff in water, but due to the size of items being so small, its messing with the code that detects its in water. I will try to fix it one day but its low in priority.
