I have a rather large farm, with water pumps/towers interspersed. The farther the towers are from the center of the region, the less likely they are to fill. The graph, I'm attaching, as the specifics. The lesser distance is where I am, in the center of the region, and the N & S towers are 147 - 154 meters, distant. The N & S Towers require refilling 2x a day, and two of them are servicing 84 small fields. Even so, they both go dry. The other pumps are servicing more foliage (trees, mostly) then the four pumps/towers N & S. I added the 2nd pump/tower N & S even when I had 36 fields, as 6 were dry; then, I added 48 more small fields, and only one field went dry ...but the towers were empty!
The white smudges, in the Locations file, show present pump/tower locations.
Frankly, I'm puzzled, given your exemplary explanation on watering of last week!
I must admit I'm not sure if there are any limits in the scripting system that would cause the problems you are seeing. The one thing that I wonder is how spread out the timing is for things, i.e. if all the plants are at the same level of water then they would all request water at the same time and that might cause a problem. To fix that just make sure to leave about 5 minutes between each planting to stagger that. Just a thought! Not sure why the further out the less likely they are to fill as if you have a water pump next to a water tower the actual position on the region of the pair shouldn't matter.
Just a final thought, there are other ways to provide water such as using the regional power system and pump. Also for the water towers that don't fill up in time you could try changing them via config notecard to MODE=SELF