My main world, the one with all the automated farms, I've been running since TU47. It is the one that got messed up with the TU54 updates and still isn't working properly. Since then I created a Creative Mode world after TU54 was released, which still has the same issues with automated farms not working properly. I now have a new Survival Mode world, built since TU56 (the thread is entitled TU54, but I built it after the release of TU56), and I've only made manual farms in this one so far, so I don't know what that one will do, but my TU54 Creative Mode world has obviously received all the updates since, and is now at the current TU62, but it still is buggy as far as the automated farms are concerned. From my observations, the problems are twofold: both the minecart coming off the tracks, as Robolist mentions here, and the farmer's black hole pockets, as noted previously, where the farmers do not farm properly.
I've just gone back to my TU47-based world for the first time in ages. I had to "flush the tubes" first, from any previous testing I may have been doing. I checked the toggle switches between the farms themselves and the delivery system, and they're all in the "on" position. I checked the deluge systems, and they were all on auto (deluge every two days) except the wheat farm, so I've now turned that one on too. I've currently got a steady stream of cactus, pumpkin, melons, and sugarcane coming through into my item sorter. I tested the entire system by throwing one Ender Pearl on the ground in each of the four farms (wheat, carrot, potato, and beetroot farms). They all went right through and I received back four Ender Pearls into my item sorter, so I have proven that part all works fine, even though the minecarts still appear to run off the tracks. While I was waiting for the deluge system to activate from the daylight sensor, I went around and activated all my semi-automated farms, including Nether Wart, Chorus Fruit, Mushrooms, Cocoa Beans, and I even let the hen's egg machine run for a short while (that one is so efficient, and the eggs only stack in 16's, so I don't tend to let it run for too long or it will overwhelm my item sorter, haha). Although I'm playing in Survival Mode, I'm also on Peaceful at the moment in that world, so I'm not getting anything through from the mob spawner, but I assume that all works fine too.
I cleared all this from the tubes just in time, as the deluge system appears to have hit, and I'm now getting wheat, wheat seeds, carrots, potatoes, beetroot and beetroot seeds coming through. The farmers in the wheat, carrot, and potato farms have all replanted after the deluge. The beetroot farmer, as has always been the way, is still sitting on his chuff, and I have to replant that farm myself. The amount of resources coming through from my wheat, potato and carrot farms is greatly reduced though, as it seems that the hopper minecart below ground is now competing against the farmer's black hole pockets above ground. I sure hope this gets fixed!
UPDATE #1: Just for clarification, up until now I have only been running my deluge system at ⅕ capacity. I have five dispensers with water buckets spaced around each farm, but only one was hooked up for each farm. As I mentioned earlier, prior to TU54, I didn't even need the deluge systems at all; the farms would just get constantly harvested and replanted by the farmer villagers. I have just hooked up the other four dispensers for each farm. With the black hole issue, I'm expecting the farmers to now run out of seeds very quickly, and I'll end up with all four farms looking like the beetroot farm, arid farmland with farmers sitting on their chuffs. The one thing that I haven't tried yet, and which could potentially fix this problem for me, is Tom's suggestion of replacing the farmers. I dread having to do that, as it is a major task, moving Villagers around.
UPDATE #2: Yep, just as I thought would happen, after the full deluge, the farmers in all three main food crop farms have only partially replanted, and have obviously run out of seeds. This would never have happened prior to TU54, when I had a steady stream of food crops coming through my delivery system constantly.