Item Drop Loss
I have been carefully watching, and have noticed that items dropped in quantity do not always aggregate properly. I know the 'No Lag' plugin worked great before, but it seems to not work so well.
I tested out my theory with my wheat farm, where I also noticed it for the first time. The wheat is collected by running water washing over the 15x16 area and depositing its 240 wheat yield at my feet (with small incident of 1 or 2 wheat lost through walls, etc). Since the 'No Lag' plugin was installed, it now yields an average of 60 - 70 wheat, roughly one quarter (1/4) of what I should be producing. The number of seeds produced is usually about 280 normally, and since the change has only been about 90.
My other medium-sized farms may also be missing out but it is less clear because the number of melon slices vary for each break, whereas wheat is 1:1.
If you need to see my example, I can show it in action.